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I've seen a few of these small frame bags which you can mount on the Top Tube of a hard tail, seen various types, Some mount above it, some below it.
Do they cause knee rub ??
Some of them mount near the Stem - Do they get in the way when standing pedalling ??? Any examples of ones which are good ?
Top tube bag - if you over pack them, then yes, you can get knee rub, depending on how you waggle the bike as you climb out of the saddle.
Small frame bag - if you over pack them, then yes, you can get knee rub. If you get the larger ones, then you can get knee rub while sitting down too, just take fewer things with you.
Stem bag - almost guaranteed to knock your knees when climbing.
Things generally only get in the way if you let them. You can adjust your position while climbing to be further back, so you are then less likely to hit them with your knees. You can also get top tube bags that are designed to go against the seatpost, rather than the stem, you might look for one of those.