Either do your 90 day report online or get someone to go and do it on your behalf. Or ignore it and pay the fine next time you go to your immigration office
You can only own a maximum of 49% of a Thai business, unless you're American and its set up under the amity treaty. You can't do any sort of work in or for the business. Only be a passive shareholder, if you want to be involved in any way, even as a director, you would need a different visa.
I'm not sure I understand the question. If you are asking if you come to Thailand on a DTV and work remotely for a company outside of Thailand, without setting up an office in Thailand, are there any implications for that company then the answer is no.
The number of passports you have is irrelevant. Passports are linked. But generally speaking you have to leave a country on the same passport you entered the country on