Why can't we just say that we discussed an application of the method for the Y model.

We are talking about 'the X method' and not just 'method', but there is something in what you're saying. OK, I'll have to revise and say, in 99% of cases (especially here because you do apply methods to model!) the usage would be:

'discuss the application of something to something'

so: 'discuss the application of the X method to the Y model'

but, yes, I suppose the X method could be an existing element of the Y model and not something introduced by application, so:

'discuss the application of the X method for the Y model'

might just be possible but even here I'd use 'used in' (or possibly 'used for' or 'used under').

Anyway, I think I've exhausted myself on this thread so will leave it there for now.