It is a valid (if highly unreadable) format, it's not being parsed as two parameters like you think though:
//if (x isin x, say yes!)
The default condition mIRC will look for is operator operand operator, from your example that works out as x isin x,
The commands are taken to be whatever comes next, that is say yes!.
The parentheses are superfluous, just working as grouping, but it'll work just the same without them.
Seeing as it's an incredibly bad format to use, it's no surprise that something similar to this would be treated as ambiguous format, why not use a more readable and structured format instead?