SMD are smaller, but more difficult to solder by hand. If you have access to a "reflow oven" for SMD-soldering (which some makerspaces actually have..) then it is much easier.
I assume that you are thinking of using Cherry MX switches. With Cherry MX, you have the choice of PCB only (switches with two extra plastic pins for PCB-mounting), PCB + plate or plate with direct wiring.
If you are using Alps, then you must have both a plate and a PCB.
With a PCB, you can use Cherry's PCB-mounted stabilisers, if you have a plate you can use Cherry's plate-mounted stabilisers or Costar stabilisers.
With a hand-wired keyboard, you will need to glue the bottom of the switches to the plate in case you would want to change keycaps, or be very careful when changing keycaps. With a PCB, the solder joints would prevent you from pulling the switches off. Of course, some switch/keycaps combinations are more tight than others...
With a PCB, if you have through-hole diodes inside the switches, then they would be even sturdier.
If your layout is quite conventional, then you could take an existing plate and cut/file away things you don't want, or enlarge the position of switch holes to move them slightly. However, if you have an enlarged switch hole and you don't use a PCB then you would want to fill the space next to the switch to prevent the switch from sliding sideways as you type. The Phantom plates have large switch holes for the space bar and Caps Lock, which you would need to fill. Plates made of aluminium are much easier to work with than steel.
If you have an acrylic plate, then I think that you would need to use a PCB, or glue a reinforcement plate to the bottom. A custom acrylic plate is much cheaper to have made than a custom plate made of metal.