@sponch it shouldn't be a problem if troubleshoot works fine.
Overall, it's become quite common now to run apt upgrade by habit or the VPS providers are running this automatically. With that in mind, we have decided to change our policy to allow apt upgrades (but not dist upgrades). We will (already have) change the platform code accordingly to adapt to different base packages as required. For Cloudron 10, the warning is already removed - https://git.cloudron.io/platform/box/-/commit/1ae9fb2477a33b724ccffb17a1fda800953aafda


