I'm curious which parts you think have deliberate non-standard pinouts. I can tell you in the decade I worked there, this was never an issue. Pinouts are carefully chosen to minimize noise, ease PCB layout, etc. To keep costs down, Maxim doesn't make a die per each package type (in general), so pinouts are designed to work across many package types. [Back lap specs change from package to package, so often wafers get allocated to one particular package at the expense of another, which in turn causes shortages in a particular package type.]
At no company did I ever deliberately make pinouts to be non-standard. If anything, if a part exists already with defined pinouts, you make it a point to use THOSE pinouts in order to steal the sockets with your hopefully superior product.
For one chip I did at a company I better not mention, a customer leaked us a datasheet of a competitors part. We actually changed our part to match their pinouts since our part was still in design. They had an interesting feature that I added as well. As luck would have it, our part came out before their part, but with the competitors pinouts and features. While we were doing high fives, I suspect somebody at the competition was pounding their fist on the conference table.