There is the whole literature Lalonde started that looks at job training and the real-world ability of quasi-experimental methods to recover experimental results:
The original Synthetic Control paper on smoking is probably a good example of an applied paper that is really a methods paper and where the empirical result is interesting in and of itself: https://economics.mit.edu/files/11859
Ludwig & Miller's work on Head Start also has some methods-y RD stuff that is interesting in its own right. I think Doug once told me about half the cites that paper had were for methods, and half for the empirical contribution: http://home.uchicago.edu/ludwigj/papers/QJE_Headstart_2007.pdf
I think of the Kremer et al. paper Incentives to Learn as being useful for the non-parametric treatment effects estimates using local-linear regressions separately across groups...but maybe that is just because that is the first time I'd seen them used well. Ditto for the Bitler et al. "What Do Mean Impacts Miss" paper, which smartly uses QTEs to investigate heterogeneity in treatment effects.
Econ is sometimes a bit hostile to "methods" papers that are neither pure econometric theory nor focused on an empirically import result. There are some notable exceptions: "How much do we trust difference-in-differences estimates" and the subsequent clustering literature; some paper someone wrote called "In Pursuit of Balance". But if readers/editors don't immediately see the usefulness of the method, it is hard to convince them you've added much to the literature. I think that is mostly reasonable - after all, I'm with Goethe on the whole "Moreover, I hate everything that only instructs me without increasing or immediately stimulating my own activity."
But because of that general hostility to "methods" papers (or maybe better said a lack of journal space for them), I think you are right that the current structure incentivizes a kind of (accidental) obfuscation, where shoehorning a methods paper into an empirical paper can be confusing to the reader about what is really important in the work. It is a tough balance for both individual researchers and the field as a whole. Although...looking above, maybe the rule is just that if your paper is on inference, you can do a pure methods paper with simulations/monte-carlos, but if it is on point-estimates, you have to do a meaningful application.