I'm not missing the point that this child will not be Welsh, and therefore choosing to call her Alice and spell it Alys is just giving her a fussy spelling.
The fact that other names have multiple spellings doesn't really justify seeking out alternative spellings of straightforward names.
As for the names you've suggested, one of the drawbacks of the name Isobel is that it can also be spelled Isabel(le).
For all the others the right way to spell those names are:
Jane
Elizabeth
Rebecca
Rachel
Nobody wants to spend their life being "Jayne with a y", "Elisabeth with an s".
I feel the same about using the fanciest, longest, most complicated spellings of Irish names, e.g. Orlaith instead of Orla, also prefer Maeve to Méabh or Medbh for children living in England.
Making a name hard to spell is stupid.