Yes, it's normal behavior, I believe. The 9.1 install should have removed/replaced 9.0.4 files in your system folder with 9.1 equivalents, but *shouldn't* have eliminated unique files, i.e. if you had certain extensions in your 9.0.4 folder that the 9.1 install didn't have (say certain hardware drivers) it should leave them there, and that's why your stuff still works. a "clean install" would have overwritten the 9.0.4 system file altogether.
I haven't heard of two "blessed" system folders on the same partition, unless it's an X/9 arrangement, but I could be wrong.