Good questions.
– Is the flat-run AeT comparable with the uphill one or should we expect alterations such as between cycling and running?
I’m the same way. Almost all of my lifetime training hours have been going uphill, so I’m horribly inefficient (and weak) as a flat runner. I know several skimo racers that are similar. Doing a flat AeT test would be painful. I’ve done them in the past as lactate tests rather to avoid the duration of a drift test. That said, the heart rates I arrived at during a flat-run lactate test were the same as an uphill test.
– Does the fact that my legs were hurting towards the end of the test, affect the accuracy and reliability of the result, even though I managed to hold the pace?
If you managed to hold the pace and have other reference points for AeT, then the results may still be useful. In that case, the issue is leg strength. (So the test may have been much more than aerobic for your legs.)
– Does it ring any bells about my overall muscular strength and endurance? Would you recommend to make any alterations in the way I approach strength (considering that I’m interested only in mountain activities)?
Only if you have performance goals for running (either flat or trail). If your goals are all uphill-centric, then I don’t think you need to improve your running strength endurance (i.e. “durability”). That said, doing any kind of muscular endurance work is never a bad thing provided that it’s supported by a lot of low-intensity volume.