I happily booted and ran an Intel Mac mini using a 4TB drive in a Thunderbolt 3 enclosure, and I do the same for an M4 Max Mac Studio using an 8TB drive in a USB4v2 enclosure (OWC Express 1M2 80G).
You'll just have to be careful to match the enclosure to the ports on the system. The base-model M6 Mac mini still uses Thunderbolt 4, so a USB4v2 enclosure would be wasted.
Funnily enough I do the same with my Intel iMac... I have a 2TB Thunderbolt 3 Glyph drive as my primary and boot drive and it works a dream... if I got one of these new Mac minis without upgrading the drive, presumably I could just plug this straight into it and apple will do its magical migration thing?