The name of the other daughter on the 1566 will looks like Julian to me (?) What does anyone else think?
I would say it’s rare to have full documentation from parish registers for a family from this time period, and missing entries aren’t at all unusual.
The current assertion on the profile that the Thomas who wrote the will has no connection to Broad Chalke is a bit harsh on poor old Thomas.
The 1566 Thomas obviously can’t be the one baptised in 1548, but at this stage I wouldn’t rule him out as the father of Amy & Agnes.