I'll abstain as I feel that modules should be written so that multiple instances of them are not even required. Like Pro_News, where each Section is equivalent to a single instance of News, with each Section having its own independent set of Categories.
If you hunt back you'll find arguments in favour written by Kuragari (original author of Pro_News v1BETA).
This approach allows some configuration parameters to be shared and some separate, with the end user/admin involved in making that choice.
It also allows you to display articles frpm > 1 Section on a single page, which is hard to do from the multiple instances approach.
The multiple instances "feature" is there in case a webmaster wants new instances of the same module with different group and admin permissions, different URLs names, different theme style etc etc.
Unless I'm missing some critical details from your explanation, all the above will be lost.
Any change at core level wont break any of your features. It's up to you, as developer, to use or not this tool ... it's all a matter of preferences.
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