Primary drive upgrade

I plan on swapping out my primary HDD with an SSD. Current partitions include: windows (ntfs), mate (ext4), garuda (brtfs).

Will a standard clone disk (clonezilla) do the trick ? or should I expect any issues?

you should. Especially on the Windows side. At minimum it should ask for your ID to activate windows again. Worst case - it will not boot+brick your device.

That is by no means the worst case scenario.

In the worst case scenario multi-booting creates an unstable rip in space time allowing all manner of nightmarish creatures access to our continuum.

For the sake of humanity, don't be that guy.