The bugs and the mantu aren't the same for a variety of reasons:
a) The manuals tell us that confed doesn't believe they are the mantu, due to various reasons that have been mentioned
b) The method they used to attack. From what the kilrathi have said in the past, the mantu were attacking at a border. They don't seem to be far from Kilrathi space. If they had had wormhole tech they would have crushed the Kilrathi at the very begining of their confrontation as they opened a wormhole in the Kilrah system and attacked Kilrah itself.
c) We kicked the bug's asses. The Mantu were capable of whipping the asses of the Kilrathi rather easily. The Kilrathi were worried, at the peak of their military power, that the Mantu would easily destroy them. One confed ship would be unable to take out a Mantu fleet of the force the bugs came in, IMHO.
d) If they were the mantu, someone would have told us
. It's not worth keeping the identity of the mantu a mystery. You don't gain anything by saying, in the middle of the third game they're featured in, "oh yeah, and these are the mantu". If anything you'd want people to know pretty early in the first game.. heck, you'd maybe even want to put it on the box... 'THE MANTU ARE COMING'
e) The Kilrathi would know. They've seen the Mantu. They've fought with them. If these were the Mantu we would have found out about it from the Kats.
TC