The accounts meta and main are in a way two sides of the same coin, one cannot have one without the other. They are also 'linked' in other aspects, e.g., display name.
Is this good? Well, it certainly could be different. It was different in the old days on SO and MO. The meta was separate, and the main Meta exists as a standalone site to this day.
Two arguable reasons for always suspending in parallel.
Users suspended on main might turn to meta to argue their case right away. This might seem desirable. But in practice it often ends very badly.
Users might not care enough about meta per se and the risk of getting suspended only on meta might not be a deterrent.
But certainly one can argue in the other direction too. Either way, currently it's not possible to suspend separately and I doubt anyone will care enough to change it.
Note though that a suspension on one SE site does not carry over to other SE sites. Only in very rare cases is an account suspended network-wide, that is, everywhere except on the main Meta.