The apps in question use a shebang of `#!/usr/bin/env python3`. I believe it is working as designed. This is a Fedora system, which switched to Python 3 a couple of revisions back. But, I would assume this would affect any system that has utilities that use that shebang.
Edit: Out of curiosity, I grepped for other system utilities that might have this quirk, and it seems like nearly all Python utilities call /usr/bin/python3 directly, but ten of them (on my system) use `env`. That might be a bug worth filing with the Fedora folks. I can't imagine they want it to act this way when a custom Python is installed. Though it's been that way for at least a couple of releases.
Edit: Out of curiosity, I grepped for other system utilities that might have this quirk, and it seems like nearly all Python utilities call /usr/bin/python3 directly, but ten of them (on my system) use `env`. That might be a bug worth filing with the Fedora folks. I can't imagine they want it to act this way when a custom Python is installed. Though it's been that way for at least a couple of releases.