Both:
Glass for 35mm to 6x4.5, glassless 6x6 and 6x9, glass again for 9x12, glassless for 4x5", glass again for 5x7"...

Confusing?

I have two enlargers: An Opemus I use for 35mm to 6x4.5 with glass holder.

For the Durst 138S I have glassless holders for 35mm, 6x6, 6x7, 6x9, and 4x5". All other sizes go in the glass holder, but a 150mm lens is really too long to print 35mm negs - especially when I have a smaller enlarger.

I have not seen any problems with flatness, even with 4x5" negatives and exposure times of several minutes ("Gymnopedie #1" by Eric Satie is my favorite timer for slow papers) at f:8