Q3A on ioquake3 multiplayer question (noob here)

Can people playing ioquake3 Q3A play others using the Steam version or original CD? Which version has the most players?

ioquake3 is multiplayer compatible with the version on Steam and the original CD (patched to the latest version.) Quake 3 on Steam is the same as the last released patch for the original CD.

Servers are safer when they use ioquake3’s server binary due to our security fixes. Clients are safer due to fixes we’ve put into place there, as well.

There should be no difference in the number of players as they are all compatible for multiplayer. ioquake3 players and servers just have the advantage in terms of security and more features.

Is ioq3 fully compatible with original engine on protocol level? (protocol 68)

The code for ioquake3 is based off the source release, so it is only compatible with the final id protocol of 68 and any new protocols we derive. New games using ioquake3 can change the protocol digits to ensure that only their clients will connect to their servers and vice versa.