This might make more sense as a wiki article rather than an official recommendation.

Nobody reads the wiki unless directed to, it has turned out to essentially be a waste of server space, but it was worth trying.

It has a couple things that aren't such good ideas like in-tree builds,

Agree that there are good reasons that experienced developers don't want in-tree builds, but they work and Geany should not be one of those arrogant projects where you need to understand all the details of the tooling before you are allowed to touch the code. Coding in C with obsolete tools is already enough of a backwater that few want to do it, so we should show how to make it easy or stop complaining about lack of contributors. </rant>

This is a simple build with minimal steps, not a perfect one, and not intended to detail use of the tools.

using autogen.sh in place of configure

Well, its for a first build post git clone, so it has to be autogen.sh and I doubt people using this are going to be re-configuring often, so it doesn't hurt to use autogen.sh again in that rare case, again its not about teaching the tools but getting people started.

installing into the directory where the source directory is might cause confusion (think if they use /home/projects as the prefix, their projects directory will be filled with a bunch of install artifacts).

The very first thing it says is create a new directory and put the source in there, maybe it needs emphasising, clearly you missed it 😁

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