First of all, putting a start.ent file into an id1 mod is not the best idea.
As you already said, lots of fan made episodes also use a start map.
You already learned how to ignore .ent files.
But what if your mod also uses .ent files ?
Then you need to create a matching start.ent file to the start map of your mod.
And you can remove the sv_entpatch line again.
Here are instructions of how to proceed.
By the way,
Did you know, by starting regular Quake, you are using: -game id1 ?

With that knowledge, you can now setup your Quake to do, as you explained:
Use id1 replacements without the necessity to have it in other mods as well.
Using multiple -game arguments is possible.
Leaving your id1 as clean as possible is always a good idea.
Enjoy your Quake.
Best wishes,
Seven
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