1) Yes, the validty of the license depends on the ownership at the moment of compilation.
However, it is against the license terms to use an academic license to develop software with the intent of commercializing it. The moment that commercialization became a realistic concern, you should have switched to a commercial license.
2) It is correct that commercial licenses are available in "perpetual" form, in which case paying for the base licenses plus compiler licenses once entitles you to continue to compile indefinitely using the same MATLAB version . The Software Maintenance Service (SMS) that is included in the initial purchase is valid for 12 months, so in most cases you would also be entitled to a single version upgrade (sometimes you get away with two version upgrades due to accidents of timing.) You would also be entitled to any "Upgrade" (bug fixes) that Mathworks releases for your MATLAB version. The number of Upgrades that Mathworks issues varies quite a bit -- anywhere from one upgrade to 8 upgrades.
If, for any reason, Mathworks decided to postpone fixing a bug until a later release, and your SMS does not cover the later release, then you are not entitled to the version that contains the bug fix. Sometimes the postponed bug fixes are fairly substantial in impact.
3) A Simulink Compiler or Simulink Coder license on top of a Standard license is enough for commercial development.
"Standard" licenses are full-price licenses that support all features (provided the required toolboxes are purchased and the platform restrictions are met.)
"Startup" licenses are reduced-cost licenses available only to new startup companies. They do not offer anything that the Standard licenses do not offer.