We have this running in our environment without issue (so far)...I just deploy only the portal.app during enrollment and then after it is all checked in... then I let the routine policy update run my scripts...do you use a script for portal.app deployment or just push the app?

I have deployed the company portal app with policy, it is .pkg file and not using any script to install it, and as i have mentioned this policy/app working for every mac OS expect Sequoia, 

do you have any post processing scripts that might be pushed out during the app rollout?  

there is no post script 

What did you use to package it up with?  it seems like Apple keeps getting tighter and tighter with their restrictions on deployment.  I wonder if the certificate that you might have used during package might not be well like by sequoia? (or any other "restrictions" the apple might have put in place

If you try to run the package from the command line (not thru SS) while on Sequoia, it will open the installer app, you can hit Command-L on your keyboard to showing logging...that might reveal what is going on as well...

I use Microsoft's Script that curls and installs the latest version each time.  https://github.com/microsoft/shell-intune-samples/tree/master/macOS/Apps/Company%20Portal

try downloading the latest package and upload it to JAMF and use that package for your deployment 

Use this link https://go.microsoft.com/fwlink/?linkid=853070