With transpose function avaiable - what tuning do you keep your guitars in?

I have two 25,5" guitars - currently one in E standard, one in Drop C. The Drop C one is getting a setup next week so i thought maybe Drop D is smarter because of intonation and action issues. Tho i noticed some noise when transposing so i am not sure. I play 95% metal, from thrash, prog, metal core....

What would you do?