There are two issues with using Geany as root, and via sudo:

the general issue of running a complex GUI program as root, where mistakes are easier to make, and especially one with plugins of various quality. And also note that it probably hasn't been tested in that very situation.
the sudo-specific issue that as @elextr mentioned: Ubuntu and derivative usually have a sudo configuration that leads to writing root-owned files in the calling user's homedir. I don't know if there's any reason for that configuration but it's very problematic in many cases. Note that it's not inherent to sudo, Debian work right in this respect.

Once you know this, do as you feel, but remember it's not a use case we support or recommend.

If editing root-owned files in Geany is something people want badly enough, somebody could research what it would take to support GVFS' admin:// URI scheme.

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