Please update xqf so it is compatible with standalone mods used with ioquake3. They don't need ~/.q3a/baseq3 or ~/.q3a/demoq3 to exist.
I suggest checking for ~/.q3a/baseq3, ~/.q3a/demoq3, or ~/.q3a/<mod name> if the user is joining a server with a mod. The first two should validate idsoftware quake3 engines and the third validates an ioquake3 + standalone mod instance.
Additionally, the error message is deceptive because it complains about a different directory when it is looking for ~/.q3a/baseq3. After I create an empty ~/.q3a/baseq3 directory, xqf will start up fine.