Steam – Do the Steam versions of the X-Com games have the original bugs fixed

No they are not, you just need to copy the complete game directory to someplace else and do whatever you want to do with it.

I modded Q2 to R1 Q2 and Q3 into CPMA in this way.

i only remember there was a discrepancy of the Steam version of Q3 on where the key file was located, but I do not remember the details at the moment.

In the Steam client:

1) Click your username from the top right, then click 'Account Details', to go to your Steam store control page.

2) From the Steam store control page, under the 'Store & Purchase History' header, click 'View licenses and product key activations'.

This page shows, in chronological order, what games you have acquired and how (Steam store, retail code, complimentary copy, or gift). Unlike the other methods above, this activation history includes any free games you may have previously installed, but deleted.