You can still run a company from Canada under these terms, the same way every international YC batch company runs --- you can just go to the YC directory and select for EMEA, LATAM, APAC, &c. There's hundreds of them.
Since this is purely about ownership structure and equity governing law, I'm curious what the intersection you're seeing between these terms and "labour rights" are. We're a US company with employees in Europe (not even an HQ in Europe, just employees there), and I've learned more about European labor law idiosyncracies over the last few years than over the whole rest of my career, because I've had to.
> We're a US company with employees in Europe (not even an HQ in Europe, just employees there)
I don't think that's true. You can't have employees without a local subsidiary. If you're going through an EOR agency, they're contractors not employees.
> You can still run a company from Canada under these terms, the same way every international YC batch company runs
Having a Canada-registered company is usually required to get government grants and loans from Canadian banks, although that's probably not very important to VC-backed companies. There are also some tax advantages to running a Canada-registered company if you're based out of Canada, plus it's much easier to find a local professionals (lawyers, accountants, etc.) familiar with Canadian corporations than US corporations.
None of these issues should cause too many problems, but if given a choice, as a Canadian I'd certainly prefer to run a Canada-registered company over a US-registered one.