Ok, I've currently implemented this so that if you import collections and the collection name has a "," in it (after the first occurrence of a-zA-Z), I convert the "," to a "\" before loading it into the custom column.
When automatically creating collections I convert any "\" to "," (after a-zA-Z). Users can manually enter "|" instead of "," in the custom column so that "," can act as the separator for is_multiple columns. I do it for plain text columns as well just to be consistent.
I'm not sure about "\" (regex flashbacks) but I figured it isn't likely to be in any Collection name and its on the keyboard though it doesn't look great. ";" would be ok, but I can't help look at that and think the default separator should have be ";"
I tried to use "|" but I get odd results. If I type it in manually or import it in an multiple text custom column it gets converted to a ",". Its clear "|" is quite special since it gets left as is for plain text, converted to "&" if a Contains Name column, and to "," if multiple. I think I'll stay away from "|"