A combination drain and skimmer section may not work. The reason being is that you will get a lot of micro and large bubbles from the water draining into your sump. Those bubble would prevent the skimmer from working properly if they get sucked into the skimmer's intake. You can prevent that with filter socks on the drain line, but you might have to make the skimmer compartment a little larger.

I would suggest picking out a few skimmer that you would like to buy down the road then size that compartment to match (both lenght width, and hight). You would be better off leaving a little room for your skimmer compartment and taking some away from your refugium caompartment, at least IMO.

Would you have your main tank drilled, or use a syphone based drain ?