"Policies that update inventory on all computers cannot be set to ongoing frequency at recurring check-in."

That's one of the first settings JAMF have configured in the JSS to help avoid issues. I can only assume it came from a number of support cases.

Generally speaking, the setting hasn't bothered me, setting an on-going frequency inventory update on all computers would cause issues.

When I need very frequent inventory data, it's normally for a specific piece of information, so I use a script that uploads to the EA via the API instead.

Can't you run a "jamf recon" command as part of the policy or a script to work around that?

Yes, and that is what I opted to do, but that isn't the point at all. JAMF needs to keep their hands out of configuration decisions. If the option is causing too many support calls, how about putting verbiage about impact in the interface, there by treating their customers like the intelligent adults that they are.