well, the point of flatpak is to have bundled dependencies so they run predictably no matter the distro

if one of your software’s dependency gets updated, and your software isn’t, you may run into issues - like a function from the library you’re using getting removed, or its behaviour changing slightly. and some distros may also apply patches to some of their library that breaks stuff too!
often, with complex libraries, even when you check the version number, you may have behavioural differences between distros depending on the compile flags used (i.e. some features being disabled, etc.)
so, while in theory portable builds work, for them to be practical, they most often are statically linked (all the dependencies get built into the executable - no relying on system libraries). and that comes with a huge size penalty, even when compared to flatpaks, as those do have some shared dependencies between flatpaks! you can for example request to depend on a specific version of the freedesktop SDK, which will provide you with a bunch of standard linux tools, and that’ll only get installed once for every package you have that uses it

it depends™

what are you protecting yourself against?

for my use case, that’d be good enough, i don’t want my school/building admins to snoop on the websites i visit, and don’t want to fear academic repercussions for torrenting and such

though if you think your government is out to get you, then tunneling to another country is probably best!

it sure seems like it though

i mean, they’ll never replace system package manager, but for desktop applications, flatpak is honestly quite good