Why does a program (HomeBank) I'm actively using not show as 'installed' or able to run from command line?

The software store has access to other types of format packages in addition to the well known .deb packages, known as Flatpak and Snap. From your description of the issue, it sounds like you've installed one of these formats and in fact the flatpak option is selected by default.

You can list packages installed from Flathub (the "store" of Flatpaks) with the command flatpak list, which will also show you the executable which you can input to the terminal to launch it. With Flatpaks this is usually much more verbose as it includes a fully qualified domain similar to how Android apps work. In this case, flatpak run fr.free.Homebank.

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