The change does get overwritten under Web/Seup/Applications/[featurename] because the post build event for mojoPortal.Features.UI copies them from mojoPortal.Features.UI/Setup/applications/[featurename] up to the corresponding folder under Web
So if I was editing a script for mojoPortal.Features I would edit the one under mojoPortal.Features.UI/Setup/applications/[featurename] and then build to move it up to Web.
However, you should not make changes to any of the scripts included in mojoPortal just as you should not modify the mojoPortal source code. Doing that creates a fork that will be difficult to maintain or upgrade. You should not add fields to existing tables nor modify existing stored procedures. Any custom features should live in your own projects and you should structure them similarly as mojoPortal.Features projects using post build events to copy your custom files up to Web. If you need a custom version of a feature you should clone it first, rather than modifying the included one.
Hope it helps,