Dunno why. I'm not proficient in coding. But he takes some measures in protecting the map against easy cheating. Removing custom artwork, and some protection against easy cp-insertion.
Nothing that will stop an experienced coder, but it will stop noobs like me, who are just following instructions.
The creator of the tool only intends for it to be used for recovering old/no longer maintained maps or learning to reverse engineer the code from the map. Hence why he has protective measures after it's done deprotecting. Of course If you're proficient In how maps work you can get around this protective measure.
Judging from the "work around" you wanted, it sounds like you want to host these cheated maps online