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Linux
Welcome to c/linux!
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First off you don't want to be downloading things off the internet. Linux systems are build with packages so you install the packages you need. Flatpaks are also packages but they are sandboxed and often are much newer versions. You can install flatpaks as a local user or system wide.
As far a security goes, securing Linux is actually a pretty complex topic. You could start by turning on the Firewall as on Linux Mint there is even a GUI for that.
For serious security you want to setup mandatory access controls (MAC). This is a really complex topic but you might be able to use defaults. Basically what MAC does is it restricts apps to only have the access they absolutely need.