One of the reasons for that practice is that modifier keys are typically pressed with your pinkie. You also use that finger for typing characters, so for these characters you need to break your habits. Eventually you build new ones, but it'd be better not to need this. Even for characters that you don't type with your pinkie, you may need to stretch your fingers in awkward ways.
Thumbs are only used for the space bar, which is seldom used with modifier keys --and you can use either thumb for it, so you can alternate. Also, thumbs are less 'coupled' with the other fingers.
I'd still prefer my modifiers duplicated on either side, but I can see how this may matter less if they go under your thumbs.
I remapped a LOT of the keys however. Caps -> Ctrl is crucial, put escape on an elevated thumb button... all the navigation keys to the "4th row"... basically I sat down and thought about where i wanted my control keys to be for easy access, and remapped them there. That solved all of my initial control key problems.
If you're the kind of person who's interested in learning Dvorak, and shelling out $200 for a keyboard, that's not much of a stretch.
The function keys are also unusually small and difficult to locate by touch (and, given the above, some function key/modifier combinations are quite challenging). The Windows context menu key is gone entirely, which means you have to use shift-F10 instead, if you need it.