I also agree with the tactical situation answer. I had a row with our former RSM over this (as much of a row as you can have with an RSM), because I always wore mine under for anti rustling reasons (and because it's described as a "liner").
You reckon they are designed to go under your smock?, how come they have the left chest map pocket opening then?. Over the top, no point in getting f_cking soaked because the enemy are more likeley to hear your moaning than the rustle of the fabric.
Wear them on the outside and be bloody grateful you can. Goretex jackets were first issued to my Battalion in 1988 in South Armagh, with a warning from our slug of a QM, that if we ripped them we would pay for them (Blackthorne hedges anyone?)My multiple spent four & half months soaking wet but the fat REMF got his jackets back unscathed (and unworn). Ah, the good old days!
I would say (in my lovely gortex experiences) it depends. I agree with MM, what's the hurry in getting stuff out of your top pockets, but if your smock's already wet - ie put gortex on a bit late, I would wear it outside.
I would prefer gortex outside and save the smock getting wet because it adds unnecessary weight, like a wet bergan (good reason for bergan liners).
I don't even take a smock on ex/ops at all in temperate or arctic climates - I just use the gortex as a combat jacket.
Quick rant: sorry, but in this day and age, cotton combat clothing is a ridiculous anachronism - what the heck is the point in using something that becomes instantly sodden - with rain or sweat - and then doesn't dry out? I know that the real reason is that cotton clothing is dirt cheap, but there have been far better solutions around for decades. Just one example: I remember being on a jump with some South African paras: our smocks were those soft cotton mid-90s jobbies which wore out in about a week; the SA smocks were made of cordura or similar, with padding & reinforcment along the forarms and across the shoulders - ie a thoroughly tough, quick-dry bit of kit. End of rant.