You _need_ to set com_zoneMegs via launch parameter (+set com_zoneMegs 48) as the zone memory is allocated before any config files are read.
Changing it via config/console makes it "latched" i.e. not in effect.
See Github.com.
48 is perfectly fine though. You don't need 128.
I also submitted a PR to ioquake3 to make this easier for users: Github.com
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