So I'll expect not having to pay VAT next time I buy from a franchised business operating in my country given that all of them usually make little to no profits officially.

The equivalent would be not having to pay taxes if you dont earn money (or lie about it which the franchise business might be doing legally or illegally). Fortunately its quite rare to have a job that results in negative income.

Unfortunately, VAT is a consumption tax that has little to do with the company. Your gov thinks you need to pay it because you consume. Are you paying a consumption tax on investments? No that would be really dumb

VAT and income tax are completely different taxes. One is a tax on income. The other is a consumption tax - like a sale tax but with additional accounting steps.