I recall reading that the Honda changes was not actually considered an engine modification rather I think an exhaust modification. I think that distinction probably recommended by a lawyer is enough to allow the change.
I assumed (and I might be wrong) that Lotus knows that this year it cannot change anything that would not be considered an "engine modification". Any "engine modification" would not be approved by IndyCar and even if IndyCar wanted to approve it they risk legal actions from Chevy and/or Honda.
It is just an assumption on my part but I just got the impression Lotus is screwed this year because of the terms of the lease contracts with IndyCar of the 3 engine makers in the 2012 season.