I asked the CAA head of GA at Aeroexpo last year and was told they were going to make some changes so the microlight hours would count, but they said that this could present problems with pilots flying to europe to a country which does,nt allow microlight hours to be counted. CAP804 us to say that hours flown in microlights did not count towards SEP but CAP804 has now been cancelled.
So the only thing left is the new ANO which as you said "FCL.740.A (b)(1) and (4) of Part-FCL, provided a SEP aeroplane with three axis control system is used."
I have also seen this mentioned in another forum that microlight 3 axis hours now count towards SEP....