Not saying it couldn't work, but I'm a little skeptical. Dwarf chain loaches are not aggressive, merely slightly boisterous, and only to very placid fish like Corydoras.
My gut feeling is that, being as inquisitive as they are, they're bound to get the puffer's attention at some point by investigating them. Then the puffers would probably attack, and the non-aggressive nature of the chain loaches would likely mean they'd get seriously hurt or even killed.
As for skunk loaches being a bit big, Botia to my understanding do not usually eat small fish, especially not more secretive Botia (like skunk loaches) that, by virtue of their secrecy, are less likely to chase small fish down. That doesn't mean there would be no problems at all with skunk loaches and pea puffers, but size isn't something I'd expect to be a problem.
Going by what Fishguy said, pea puffers may be able to keep pace. But we'd need someone to try the mix to know for sure, though.