You don't need to select all of your products from the bulk UI, just the ones you want to sync hourly. The rest of those products can be set to whatever app you want (I think the default is "Shopify"). As I said before *The bulk edit UI is the only place where the hourly inventory settings actually take effect*. You mentioned "going to those products, changing the inventory managed by to the app and then checking the track quantity checkbox". As I mentioned before, this does NOT work for hourly syncing.
I may have misunderstood what you're saying though. If you've also tried making these changes in the bulk UI explicitly, and you still don't see hourly syncs, then it is likely a different problem.
Sorry "*The bulk edit UI is the only place where the hourly inventory settings actually take effect*" is the important sentence here. I genuinely cannot believe that this would be the case and that shopify wouldn't be on this bug to fix.
I will do as you say and report back.
Thanks again for your help, and I really hope this fixes it!