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Not familiar with the Mobile Server technology myself, but I'm guessing that you intend to install APEX on the database server that you synchronize with. So, based on this assumption:
1. You can create an authentication scheme based on your authentication framework used. See documentation.
2. Create authorization schemes to control page access. See documentation.
3 & 4. Sure you can, but you're probably in the best position to figure this out.
5. Definitely. You can customize your own APEX themes or tweak existing ones to suit your corporate requirements.