TB is following a common method of updating the software which is that it automatically identifies the availability of updates and then urges the user to perform the update. At least that is how mine has been set up. Portable apps has its' own method of identifying available updates and then urging the user to perform the update. Do these different methods conflict with each other. Is one or the other invalid or maybe we should say NOT applicable?
The platform is the preferable option as it will also update the portable launcher (ThunderbirdPortable.exe) with bug fixes and improvements, but the built-in updater in Firefox and Thunderbird will also work portably.
Typically, the update is available in the platform before the app will prompt you for an update, but app updates have been running a bit slow as of late due to outside issues. Thunderbird Portable's update was built and mirrored last night. It's being posted shortly.
Sometimes, the impossible can become possible, if you're awesome!