Does Quartus (13.1) synthesizer supports configurations ?

Have you tried separating the two architectures into two files?

Configurations are not something you see people use very often. Usually people make entities with generics and use generics/generates to control what actually goes into the modules.

But configurations should work, although I note this issue from 2012:

https://www.altera.com/support/support-resources/knowledge-base/solutions/rd07032012_70.html

Configurations have been around a long time, so should work. But alas - I never use them, so cannot test for you.

Have you tried a newer version?