Since Welsh names were in a time of transition at this point, I'd recommend use of a ===Name=== section in the biography where Jane's name can be discussed and clarified.
Because the Welsh culture was essentially being suppressed by the English, you can expect that for several generations, the Welsh culture would continue "underground".
What was her last name at birth? If you can find a baptismal record in the local church, it may well have been in Latin and said something like (Latin form of Jane), daughter of (Latin names of parents) was baptized on such and such a date. That basically doesn't help you!
What was she referred to in her community? Probably, Jane, Owen's daughter. (And did they use the English spelling Owen or the Welsh Owain? And of course if the sources are writing in English they'd tend to use the English form. Even if they were using the patronymics, they'd be likely to write "verch" rather than "ferch" because it sounded like a v to the English.
I think the 1535 date was the date of the order by the English, which was then implemented over a couple of generations, during which you'll find uses of both forms.
Again, as you've discussed, what to put in the LNAB field is going to be arbitrary because both were probably in use. But have a Names section where it can be mentioned!