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It's not papering over it if you look at the rest of the paragraph. The problem is that the IDEs just aren't made to work with this kind of sandboxing and need to be changed significantly. I agree it would be cool if someone eventually made an IDE that could operate like that.

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My point is that I work like that with current IDE's when using Qubes OS.

What I suggest is that Flatpak could provide something similar, by having a completely separate filesystem used by the tool.

That would need UI similar to Qubes that would have to be built and integrated probably on the IDE side. Purposefully, flatpaks don't typically ship a whole OS like Qubes VMs do, so the gap has to be filled somewhere.

Most VMs in Qubes does not come with a full OS. They're based on templates, which isn't too different from the system packages of Flatpak.

Also, Python developers seems to be dealing with this stuff on a daily basis with virtualenv, so this isn't something new.

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