Considering that you’re gonna go with the link ECU and harness, it really doesn’t matter which you start with (auto or manual) since the link can work either way and still control the factory climate control and cluster.
Autos will probably fetch lower money initially and then the extra money you saved not buying a manual IS you can then buy a manual transmission swap.
Alternatively, finding the cheapest manual (if that exist) you can find that has a good body would work too as for obvious reasons makes changing to a different manual transmission easier but you will still need to pay extra for said “upgraded” manual gearbox.
Autos will probably fetch lower money initially and then the extra money you saved not buying a manual IS you can then buy a manual transmission swap.
Alternatively, finding the cheapest manual (if that exist) you can find that has a good body would work too as for obvious reasons makes changing to a different manual transmission easier but you will still need to pay extra for said “upgraded” manual gearbox.