I'm not sold on it. In my opinion, if the pot is too large for the plant, bottom wattering can do more harm than good by keeping the soil below the roots soaked, you are just asking for a case of root rot.
On the other hand, for little seedlings, it can be a good thing because it keets the top of the soil dry and this is good not only for damping off, but it also keeps fungus gnats from laying their eggs in the damp soil.