As for the tune, you get much more of a benefit with an AT since it helps remove the delay in the computer when shifting/giving it gas.
As for engine mods, they are not MT only; engine mods mod the engine, which has nothing at all to do with the transmission. The only thing in terms of engine mods that depends on whether or not you can do them is what kind of engine you have, and since you have the 1.4T you will be able to do a nice amount of mods to drastically improve your Cruze's power. The only thing that you wont be able to do is a short shifter upgrade, or a clutch upgrade which can limit the amount of power mods you can do before your transmission cant handle the extra umph. But there are still a lot of possibilities for you to take advantage of.