Hi,
I'm glad you like the module! ;)
You can't currently "mask" the index page, if you'd like that functionality to be added please get in contact privately.
That's the beauty of "URI mapping", it is totally fine to do that!
No, there's no point in my opinion!
On a separate issues, the module only uses the URI mappings in links for the products, categories and EZ-pages, the "aliases"/"alternate uris" map to a particular page but the modules doesn't currently catch on to other Zen Cart pages and replace their links with any alternate URIs. That functionality could be added though.
You're very welcome!
All the best...
Conor
Ceon
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