Two details.

First of all each script is created in its own namespace. So one script's package globals should not interfere with anther if you don't influence variables in packages.

But if, as above, you influence a variable in another package, then you can get conflicts. To make this not a problem you can use local. As in:

local $CGI::DISABLE_UPLOADS = 1;
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Then when your script runs it will properly localize its effects.