Why can’t the installation create aliases like

flatpak run jellyfin-media-player ? And then highlight conflicts during?

This is extremely simple to fix with scripts that can be automatically created on install time. Here is a quick script I just wrote. It will search for first matching app and run it. Just save the script as flatrun, give it executable bit and put it into $PATH. Run it as like this: flatrun freetube

#!/usr/bin/env bash

# flatrun e
# flatrun freetube

if [ "${#}" -eq 0 ]; then
	flatpak list --app --columns=name,application
else
	app="$(
		flatpak list --app --columns=name,application |
			grep -i -F "${@}" |
			awk -F'\t' '{print $2}'
	)"

	if [ -z "${app}" ]; then
		flatpak list --app --columns=name,application
	elif [[ "$(echo "${app}" | wc -l)" -gt 1 ]]; then
		echo "${app}"
	else
		flatpak run "${app}"
	fi
fi

Edit: Just updated the script to output the list of matching apps, if it matches more than one.

It’d be dangerous if an installed app claimed to be something like sudo or bash. Even if a mechanism was created for flatpak apps to claim a single shell command, there is no centralized authority on all flatpak apps to vet them. If there was for flathub, and each uploaded package was checked, that still leaves every other non-flathub flatpak repo which must implement the same vetting. Because there’s no way to guarantee to do it safely, and because flatpak devs are unwilling to compromise, this is just what we get.

https://github.com/flatpak/flatpak/issues/1188

flatpak run com.github.iwalton3.jellyfin-media-player

You can use /var/lib/flatpak/exports/bin/com.github.iwalton3.jellyfin-media-player instead. and then create aliases or symlinks (for example in ~/bin/) for that.

https://github.com/boredsquirrel/flatalias

Or my PR for that, that makes aliases on every login. I just have to fix it to work with user flatpaks as well: https://github.com/bjoern-tantau/flatalias/tree/patch-1

It would be pretty neat if they did like zsh does, where it asks you if you mean a certain command when you only type it partially.

You can create a alisis

you're missing a directory from your PATH if you have to do that. flatpak Has friendly names

There's a reason security people don't use flatpak, but that's not it.