Yup. The big downside to flatpak is that, as you said, it takes up more space.
To make a Windows comparison, imagine needing to install Java separately for every single program that needs it. Flatpaks tend to be orders of magnitude larger than technically necessary, simply because they’re sandboxed and come with everything they need to run, even if you already have it installed.
Microsoft took a big bite out of GRUB, which is the utility that your motherboard uses to dual boot OSes. A Windows update basically borked it and set Windows as the mandatory default OS. It basically makes it so your motherboard can’t properly identify your Linux install(s).
Luckily, you can fix it directly in Windows Command Prompt. But still, it’s a dirty trick that Microsoft has been using recently. Windows has historically been a bad neighbor for other OSes, (for instance, the Secure Boot Module is basically an attempt to make booting other OSes difficult,) but this was the first time in recent history that they have outright prevented another existing OS from booting.