You yourself wrote that it was complex.
The code that was modified was complex to understand, partly due to poor documentation. The changes made were not that complex and I also tried to document them appropriately, as well as inserting or revising documentation to try and make the area more clear for future maintainers. The main concern is a lack of testing (as with all changes), however from a brief test I ran I did not observe any unusual or broken behaviour. Additionally the original behaviour which was changed could be considered buggy (inconsistent counts) so it cannot be any worse.
Combined with the growth revision and factory revision I think this would make sense to be bundled with them.
I think walking is exactly the right penalty for covering entire cities with a single stop.
Except the problem is that within a single stop you can still get walking occurring. For example I cover an entire city with 1*12 subway stations (each a separate stop, linked by regular subway service) and was still seeing 1,000 odd passengers walking at some of the stops. This is especially important for inner city consumers which can easily pull in thousands of passengers per standard month from a small area. Such passengers are effectively not transportable so the players should not be penalized for them, after all they are still making it to their destination thanks to the player in some way.
Next to the growth penalty and loss of potential profits (or losses, in some cases) currently there is no penalty for covering entire cities. Most of your profit will be earned by inter-city lines which are unaffected by walking. An efficiency financial penalty would be better for hugely spread out stops of disjoined parts because it could force a time where it would be cheaper and more profitable to have separate stops linked by transport. Such a mechanic could be considered at a later time.
I also added some easy to fill in tests if you want to change or expose the walking mechanics as a game option. The current default is to count walked as transported which means all recorded metrics should add up. The other branch is to remove them as transportable which will mean that the metrics no longer add up to the total potential passengers in the system but city growth is still based on actual shippable units so is not penalized for walking.