1. you cannot install the same module in a DNN installation twice. however, you either may add a (host) option to select proper mode per instance or globally OR you may include multiple module definitions, where a host may use "Premium" feature to control, which one is available per portal. Third option might be a feature depending on licence, if an appropriate licensing solution is used.

2. Upgrades are handled by using incremental sqldataprovider files and cleanup options in manifest (DNN5) or file (DNN4). Manifest contains module version (needs to be specified in code as well) and DNN extensions installer prevents installation of previous version (no downgrades!) or on inappropriate core framework version (partly). Scalability mainly depends on your development skills: use adequate SQL and caching.

I meant, you are able to implement a setting (per instance, per portal or per installation) and adjust your module rendering accordingly - Like forma and List module provide a switch between form and list and options accordingly.

If you want to deply your module, you need to package it with a manifest, you may start with an automatically created manifest (use the option in Host :: Module Definitions on a local installation) and tweak it according to specific needs.