The 13 round magazine is larger than the 10 round. What they're implying is that with the compact you can have the same magazine capacity as the full size(since the full size 13rd will work with the compact but will "stick out") or you can use the smaller 10 round magazine(which is intended for the compact and "fits flush") for compactness.
When considering porting, you have to consider where the flash is being redirected and the drawbacks to it. Size depends on what purpose you have for it. You are better off with the largest one suitable for your purpose. You may also want consider the regular size as a compromise between the two(service and compact). You should take a look at each example in person to get a good understanding of their actual sizes.
ETA: I just noticed you also posted the USP question. Same applies to both.
Are you more specifically looking for a "high capacity" .45 ACP?
Forget the porting, this gun would double as a self defense and did not think of the obvious night issues.
The XD 45 Compact has the two different mags basically for concealment ease. With the 10 round mag in, the grip is a lot shorter and will print less than if the full 13 was in. But when you go to the range or when the gun is at home, you can slap the 13 in and you have more ammo at your disposal for home defense or less reloads at the range.
S.A. Wanted to quickly get a small short bbl.and short grip CCW handgun to market. And the short bbl. they were working on was having problems as do many other Mfg. short action short bbl. handgun have. So having a good working 4" in the XD-service they cut the grip down and came up with the short Mag. It's the same good to go 4" XDs with a shorted grip.