Cyanogenmod is/was more or less pure Android. So you can assign file associations like in any other Android version, e.g. also in the Cyanogenmod successor LineageOs. I just checked in my old CM 11 = Android Kitkat 4.4 and in my LineageOs 14.1 = Android 7.1.2. Both handle it in the same way. So the question is: which app is currently opened by a gpx file. Then go to Settings->Apps, tap on that app, which opens app-info and scroll down to "Default start" or similar. There you can "Reset Actions to Standard".
Next time you tap on a gpx file a menu is opened which offers the possible candidates. In my case for example Navigator and Oruxmaps. There is also an option to "Set as default app".
At the beginning, there was no other application than Navigator to handle gpx file on my smartphone.
In Navigator - Settings--> Applications, "the default start" option is greyed out and I was unable to change this setting even when I deleted and downloaded again Navigator.
So I downloaded a different application, i. e. GPX Viewer to open .gpx file and this one was automatically recognised by Cyanogenmod as a candidate to open .gpx file, but still no way to change the settings of default application.
There are more dependencies. Both on my previous Samsung S5 mini as well as on my current Moto 5Gplus, I have no associations to choose from using the default file manager.
From Total Command I can open with the 2 installed nav apps (and pdf viewer?).
You may be right, as I was using ES Explorer where it worked and showed my 2 navigation apps. Using the builtin cm11 file manager I get only the choice of editor and oruxmaps, Navigator is also missing here.
The Android OS as such does not support mime types. By now there are about 1 million. It means that the application must tell via the ACTION_VIEW option which mime types it supports.
I do think that MapFactor does it correctly. How would "good" file managers know which applications to choose if MapFactor would not let them know?
I assume it is a bug in the very limited stock file managers.