Hi Judy,
I should probably step in here as I am using one of the programmes which does introduce multiple spelling variations together - Fiona Nevola's Oxford Sound Reading programme. However I still consider myself as a on a steep learning curve with the programme and SP in general, and haven't taught that many pupils to date, so these are just my thoughts based on my experience to date.
I understand that the main UK programmes which do introduce spelling variations together are OSR (1:1 remedial programme) and Sounds-Write (classroom programme). These are based on Diane McGuinness' analysis and organisation of the alphabet code and her research into learning. The multiple spellings also tie into the approach of saying this is the sound /or/ or whatever and these are various ways to spell it. They are likely to use the label linguistic phonics to differentiate from SP. They also don't use terms like long/short vowels etc.
This means they share similarities in structure to 'that programme'. Diane's book Why Children Can't Read' was written after Jolly Phonics and possibly Mona's Step by Step so these programme were based on different 'architectures' as Dick has described them. I know from Mona's book, which I am currently reading, that Sue Lloyd had taught with the ITA, so that had an influence on the structure of JP.
For the OSR, the programme is divided into 2 levels, for beginners (up to RA of 8ish) and more advanced learners - often better readers than spellers. Until this term, I had only worked with pupils at stage one where the main spellings are introduced but not all spelling alternatives. What I have found is that pupils do learn the code well for reading and can usually make good progress of decoding and reading individual words for the sound we are working on. However, if they have underlying blending difficulties, they may still find reading text quite hard by the end of the programme. If a pupil is a good blender they can progress very well.
I has just finished the programme with a 7 year old who has made a gain of a year on spelling (Parallel sp test) and 3 and a half on reading (Individual Reading Analysis). However, she still needs to sound out quite a lot so isn't fluent she also makes some errors with similar sight words and occasional misreads vowels, so I am giving her BRI, which is so good for sorting these things out.
For spelling, she was able to finish th year 3 test and give a possible appropriate spelling for each word (big progress) but not nec the correct one (!)- so that is where we need to revise now. Now she has the code on board for reading, I am slowing the pace up for spelling and I may suggest her parents work on 1 sp alternative at a time for revision. I'm not sure how long I should suggest they spend though - we'll have to try it and see. She does seem to be picking up things quickly now - there is definitely self-teaching going on. Perhaps because she is younger?
If a pupil is a beginner and shows difficulties with blending (or has concentration difficulties). I will now be more likely to use the BRI reading books. I am finding these books excellent as the children constantly practise blending with old words, as new ones are gradually introduced and there is a lot of practice at CVC level, with 4 sounds words gradually introduced. In addition, this is within connected text ,which as the reading thread shows, is where all the guessing problems surface.
So now, that I am using these books with about half my pupils I am trying to produce spelling sheets to tie in with the order in the books. I am planning to do a set after each set of books. This will then reinforce the code we learned for reading (and I do informal spelling work on the whiteboard).
The set I have been working on does have a few spelling variations within a set but certainly not all. These have been based on the order of use in the language I believe. So I believe this more in line with other Direct Instruction remedial programmes like Step-by-Step and the Sound Foundations materials. I am finding this more appropriate for the weakest learners. It also means that it is easy to give parents materials to use in between lessons.
I have just started using OSR this term with 3 more advanced pupils at Stage 2 who read at a level beyond ARI. I have found it excellent for working with a yr 8 pupil who is a pretty good reader but was guessing unknown m-s wrds. He is a good speller but in his own writing tended to reverse letters (he is dyspraxic) and missed out syllables. I have focussed on the most important sounds and he has coped fine with multiple spellings. We have done lots of m-s work and no-words for reading which has helped him hugely. I used your non-words Judy - many thanks.
My other St 2 pupil is in yr 5 and reads at about age level but his SA is about 2 years behind. I feel he has made definite progress in his confidence, in saying sounds instead of names, and understanding how the code works but the sticking point is getting the word-specific learning into his long-term memory. It has been hard for him to keep up with the sheets, as he has a higher workload from school.
So I have decided to give to spend 2 weeks on each sound, giving him the Stage 1 sheets first, so at least hopefully he will become more secure on the basic words and the most common spelling variations. I think the key is writing the words often, so hopefully this slightly slower approach will help here. So I suspect that for many pupils it may take say twice as long for spelling gains to match reading gains. Whichever approach is used, structured repetition will be needed.
One more point, Judy which hopefully will be comforting

, is that however slow the pace might seem to you, it will be faster and much more logical and effective than the traditional dyslexia programmes. These take forever as they include consonant blends (and often rimes now), vowels are taught one at a time etc and when you finally get to m-s works you have the syllable types etc!
All with no decodable text to really reinforce the blending skill and code taught - which I believe is vital esp with the reading scheme books which children will be getting at school. These rogrammes are v good on dictation though. I actually feel they all come more from a spelling perspective, which is why so many rules are included.
Sorry, this ended up being so long!