I would say that they encourage the flatfile one by indicating is it the least intensive, so if you are looking into which to use for cutting down on load, it appears based on what they are saying that it would be less intensive. I do not know anyone using this method to determine if what they say is the case or not.
The flat file one concerns me, however, due to it being files on the account itself, which are then open to being hacked and your information might then be compromised. As the MySQL system to do it instead would be less a security risk (even if more intensive than the flat file one), I would myself go with it. I would wonder, though, if adding this caching using MySQL will simply have similarity of load to not having it at all (or how many queries you would run using this in comparison to not using it).
Basically, either of them has risks (security for the flat file which will not be in the database but files on the account; queries increased or load being the same for the MySQL one as well as increasing the size of the database itself), so whichever you choose you would have to decide which ones you prefer to take. Otherwise, simply don't use it. If your forum isn't that active and you do not have a lot of mods, I am not certain you would need to use this or not.
Sorry if that might not have been helpful, but that is how I see the choices available
