There aren't any "hidden" bonuses for the races.  All of the inherent abilities and starting techs can be seen in the race setup screens, but you can also view them in the RaceConfig.xml file as mentioned above.  When playing against them, they can have additional boosts in economy and production depending on difficulty level.  However, those can be seen in the race setup screens as well.  The only thing I've found that isn't obvious is they can start with a number of colonizers for higher difficulty levels.

In DA, there's a fairly significant advantage playing as a stock race as opposed to using the custom race.  For example, the Yor and Thalan get get an excellent set of starting techs and have some really nice inherent abilities.  Those can be easily viewed when setting up ability points.  You can't get nearly as much of an advantage using the custom race.  In TA, I've found there to be less of a disparity between the stock races and the custom race.  There are more options for the custom race and the stock races don't get as many starting techs and inherent bonuses.

BTW, all this only matters when playing metaverse.  For non-metaverse games, you can simply set up a mods folder, select "use mods" then run a customized RaceConfig.xml with whatever bonuses you like.  However, be careful not to modify any files outside the mods folder or your games will get flagged as cheats when playing metaverse.

Well, it's +2logistic vs 4 points trade.

Another reason to play Torians is to not have Torians as enemies. Otherwise AI Torian could snatch Aquatic Transport  Station glactic achivement for himself (if playing ToA).

Then, there is matter of starting homeworld. Torians have small edge here.

Torians start with 9 PQ word with rings and have 6 PQ planet nearby.

Custom race starts with 10 PQ word with moon and 4 PQ planet.

Personally, I think Torians are balanced as is. It's more an issue with Custom Race having all super abilities valued the same. While obviously some abilities, like Super Breeder, are much better then others.

You haven't mentioned which game you're playing which makes a difference, but in any case, not all races are created equal, custom race included.  The developers have never made any claims they're supposed to be either.  One of the advantages of single player games is that balancing is not as critical.  If GC2 was multi-player, I bet the devs would catch a lot of flack regarding race setup.

I think the idea is to find what works best for how you play.  You may very well be right that Torian has less of an advantage over custom race, and so you should play custom race if that's what you prefer.  Personally, I've found super hive to be the most beneficial ability for my play style.  In DA, I can't get near the advantage with custom race as I can playing Thalan.  In TA, I still like super hive so I'm sort of pigeon holed into custom race because it's the only way to get the factory buildings it works best for right out of the gate. 

Again, all this only applies to totally stock or metaverse games.  For non-metaverse games, you can configure races however you like so if you don't like the way the stock races are set up, just mod them.