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It depends on what you want to do, doesn't it. With an MTB or the more adventurous road bikes the trend is for short stems. So to my mind you decide whether you want a full-blown roadie build with 120mm stem or a gravel/whatever build with a relatively short 90mm stem and better handling on slow, technical gravel stuff.
And a longer seatpost is more comfortable all else being equal.
Frame bag space is the remaining consideration as you say.
Do you need frame bag space? I always size down. Prefer the handling with a 120 stem over a 100 or so