I use the flatpak version of Obsidian already for a year or so and didn’t encounter any problems: like you I’m running Mint.
In some cases I use deb or appimage, example, if an app is unable to use my GPU fully, like for photo/video editing, 3d rendering or simply bc there’s no flatpak available. Otherwise I use flatpak. If you need to configure flatpak, use the terminal or Flatseal.
Of course you need to take in account, flatpaks are bigger, because they ship with their own libs and runtimes. The advantage is sandboxing and frequent updates.
I wouldn’t think twice - make yourself a picture: simply download and try Obsidian, instead to lose time with worries. Obsidian works well for me on Mint cinnamon.