Do top schools take these tests into consideration even if you are applying for a junior transfer?
As for actual requirements for junior transfers, you must check each college to which you intend to apply. Most high ranks, such as ivies that take transfers, require and consider test scores even if applying for junior transfer. And for that purpose, most of those will consider tests taken while in college, while some will look only at test scores taken before attending college. Outside of your high ranks, large numbers of colleges either do not use test scores for junior transfers or give them little weight, but even those usually use them for sophomore transfers.
Check the Common Data Set, section D, for each school.
For high ranking schools however, is a low test score cause for them to just toss your application aside even if it is a strong application?