I am shooting a Nikon Z8 and Z 105 MC in an Ikelite housing with the 50 mm extension and Macro flat port. I have about 3 mm of space between the end of the lens and the back of the port glass. The port has 67 mm threads. Am I able to use a Nauticam MFO-3 and SMC-1 with this setup?

You can certainly use the MFO-3 it comes with an m67 adapter to allow it to work on any m67 port. The basic option would be screw it on when you need, but I expect you'd be a lot happier with a flip adapter or some sort of bayonet system - I'm not certain but the pics of the flat port look like it should take the Nauticam bayonet adapter but you would need to check the adapter will fit over the lip of the port. If that works, the SMC with a Bayonet ring should also work. Whether it works will depend on how wide the lip is on the end of the port is (where the M67 thread is) as the Nauticam adapter fits over the lip as it screws on.