It takes effort. Presumably all of the people involved in Gentoo are already busy people and running your own IRC server is just another task they don't have time for.
Add to this that potential users then have to discover YOUR server and use it, rather than just 'all the open source project IRCs are on freenode', and it's a big hassle.
None of that is insurmountable, but they have to apply their effort in the most efficient way possible.
Not to mention that "running an IRC server" isn't just a technical job, it's a social one. You have to interact with channel owners, ban abusive users, combat spam etc. Much more efficient and convenient to consolidate all that into some sort of community.
Add to this that potential users then have to discover YOUR server and use it, rather than just 'all the open source project IRCs are on freenode', and it's a big hassle.
None of that is insurmountable, but they have to apply their effort in the most efficient way possible.