MyAnimeList sources and curates their data manually with the help of their staffs and users.
Their Frequently Asked Questions stated,
I can't find a particular anime/manga entry on MAL.
First of all, make sure the entry meets the Database Guidelines. Foreign productions (e.g. Avatar, Original English Language "manga") and Korean ...
This is based on my opinion and my experience with MAL
Mentioning for the sake of context: One of the main function of MAL is a platform for anime viewers to come together to share their knowledge, reviews, opinions, recommendations etc., and also to keep track of a list of animes that they've watched. The site doesn't do anything by itself, as the ...
On this reddit thread, you can see state of top anime list since 2007 until 2016. According to it, FMA: Brotherhood was outscored by Gintama at least for some period of time.
This history thread is not up to date, but at least it answers your question - yes, there was another top anime since FMA:B was released.