As YunZhu stated, the correct aproach is to make a setup page (card) for the extension where u can activate or deactivate the functionallity per company with a boolean and a procedure to get the enabled state from, in every place that is needed put a:
if not enabled() then exit;
and end the functionallity based on the configuration.
The extension will be installed in all the companies, but the functionallities/pages will have a validation checking if its activated, this way
↑ This is the correct aproach in 95% ~100% of cases
The other 5% could be a personalization extension where specifically u just need 1 functionalitty on 1 company, so u do the if getting the company.
But even in this case i would go with a setup page, for the posibility of new companies in the future.