Difference over 25 miles between disc and 88mm rim would be a few seconds,if you want a disc get some ralteck covers plenty of people use and recommend them.
It's possible to have a fixed /geared bike but a lot of faf changing from one to the other.just build a fixed TT bike and try it for a season you may find that is all you need.
Never known anyone get disqualified for being over the 3 cm rule half the people in the average TT would fail .