This is interesting @MoreTrafficChaos and you have had a lot of good advice.
Some will weigh more heavily than other tho.
I think your DCS' PoV to want different things is very valid - I can imagine that if you are a twin, you are more than ever keen to strike out on your own. What is it that DT2 specifically prefers about school B? Is it valid (ie not 'I liked the head teacher's pink jumper' but more 'I want to learn Spanish/do coding club')?
I have had DC secondary and DC with varied interests and I think most of the issues flagged about the headspace/admin of two schools would not carry much weight for me.
I agree with @UsingChangeofName that parents evenings on different dates would be a GODSEND; secondary PE are such a PITA even with one child. So that's deffo a positive. Might be worth finding out what day they do them on tho (my DCs' school was always Thursday) as if it could be the same day it would clearly be impossible.
I think for me the issues around collecting money, inset days (secondary kids are fine on their own and mine usually organised something with friends), PTA (don't get involved- most parents don't - or take it in turns if you are keen), Christmas and summer fairs (not often held in secondary tbh), IT systems (?), uniforms (just buy each the right blazer, no hassle), and theme weeks (again not often a thing) are red herrings and not things I would personally mind having to deal with.
One issue might be concerts - if you have very musical DC then you will be setting up for several years of either clashes (divide and conquer) or two concerts in one week (suck it up). It's manageable tho I reckon. Also the same thing for sports fixtures perhaps.
I agree you need to make it clear to DT2 that if they get into school B, they will not be able to do after-school stuff - this might be play rehearsals for example, would this be an issue?
I see the point of ppl who say 'I choose, I'm the adult' - but given that these DC have expressed a preference, it seems a bit unfair to say to one 'well that's tough.' Talk it through some more - and the questions for schools idea is a good one.