Yes it's true there are 2 MC-Server-Apps but unfortunately they are useless for the serious used one. I use custom jars for the minecraft servers and a lot of plugins. All this must be manageable. The best way is a clever FTP or even better a reasonable webpanel which allows up- and download of the plugins, custom jars, start parameters and much more. Furthermore, a proper rights management should be included so that if you have a large team, you can give read and write access to certain folders to individual people and or start stop restart rights for the server.
There is just so much missing in the MC apps that it's crazy. Also they should not only be able to use the vanilla port because there are some plugins like Dynmap, Plan etc. which need more ports to work. For this a Portrange would be very practical.
At the moment I've made a Multicraft with Lamp and use it, but because of the missing portranges and the strange rights management of the app I can't autoupdate it and I have to be careful when I make a backup without explicitly checking the folder rights before the backup doesn't start because it doesn't have the necessary rights.
All this leads to the fact that I have to tinker around a lot by hand to get all my MC servers online properly. Not to mention clever mysql...
translatet with deepl i hope its all understandable =).