I have struggled with same issues...and went with my primary kit storage in soft bags (Wolfman tank bag, GL Great Basin "U" bag, and small utility bags on the engine guards) on my KLR.
But...also have a medium sized Pelican case on rear rack. This provides at least some bombproof, weatherproof, lockable storage on bike (and covers the OEM tool roll).
I like a modular mix of "solutions"...some or all of this kit and cases are on the bike at different times. For the main part of the journey...it's all there. Local touring...much can be taken off and ideally left at a secured location or with responsible friends.
I agonized over hard or soft...but honestly, look at the locks/latches on a set of hard bags. Easily defeated.
I also agonized when the bike has be lying on my leg...and been really thankful for soft bags and good boots!
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