Should I simply reverse the pin mappings? It doesn't really matter for my application since I can just change the software to remap it automatically for me.
It is almost always easier to fix things in software than hardware. A lookup table is quick, easy and obvious.
Is it considered bad practice to use "weird" pin mappings for ease of routing?
Excuse the rant but this is a pet annoyance of mine...
There is
no such thing as "good practice" or "bad practice", and people who declare things as either without context are generally dickheads with a narrow, sometimes quasi-religious viewpoint and should generally be ignored and/or ridiculed.
Every application has different requirements and priorities, and any implementation is always a compromise based on those priorities. More useful terms might be "more appropriate" or "less appropriate" to a specific set of requirements.
For example in the above simple case, fixing in software would typically be the best policy as it simplifies the hardware, maybe allows fewer vias and/or shorter /wider traces (all of which are better for manufacturing yield) , makes the board smaller, may use fewer layers, and has negligible impact on performance.
However if the PCB was going to be used by many different people writing their own software (or in an environment like medical where everything has to be documented in extreme detail for approval), it might be better to have the pins in a logical order, as a scrambled order requires more documentation. Similarly if the processor was likely to be so full that every last byte had to be squeezed out, a hardware fix might be more appropriate. Or if you were driving something that needed very fast update which couldn't afford the time to juggle the pins in software.
Maybe the board already needs to have more layers due to other aspects, which might eliminate any additional cost or complexity in arranging the pins nicely.
Something I've yet to see any PCB tool handle nicely is the concept of "These two groups of pins can be connected in any order, juggle as appropriate to make the layout nice", so it's one of those things you need to learn to do manually.