Basically, Hitachi and Motorola, much like land fiber based phone companies, they love and hate each other, often at the same time. On one hand everyone at the cutting edge of tech has to be on the same edge, and certain lucrative .gov contracts require second sources for hardware so they have to cooperate, on the other hand the bean counters see it as an income stream to sue each other for infringement, possibly as a merger strategy gone bad, or just stupidity and arrogance, who knows.
From memory, Hitachi sued Motorola over their 68hc11 microcontroller infringing Hitachi's patents primarily as punishment because Motorola licensed all their pre-'86 CPU technology to Hitachi while Hitachi was of the opinion Motorola falsely post-dated a bunch of hardware features post-'86 literally to F them over when Hitachi marketed their H-8 and H-16 processors. Somehow this lawsuit battle continued into the 90s with Hitachi threatening injunctions on Motorola shipping 68030 processors which were used in early Mac computers, that made the news. In the end, nobody was successful nor made money other than the lawyers.
So in summary, if somebody permits you to second source a design even though they hate you and are in a battle to the legal death with you, and you're like "LOL I can trivially make a 2.0 improved version of this old POS" then depending on how the legal battle is going later on, you might just ship the silicon and kinda not talk about how its a 2.0 improved version that's faster and lower power and new features.
Or in a summary of the summary, the two companies loved/hated each other and there were so many weirdly worded license agreements and open legal cases, that its not entirely clear what was legal or illegal about manufacturing a "2.0" of someone elses processor design.
So why did they put all those extra features in at all? My guess would be that they had a big buyer, who was in a position to write their own software to make use of those features. This is why you end up with undocumented features in Intel chips today, and the buyers are either big datacentre operators, like Google or Facebook, or government organisations, like the DoD or NSA.
I don't know who such a buyer would be for the 6309, though. It came out in 1982, the same year that Intel released the 286, and Motorola released the 68010 (and National Semiconductor released the NS32016). Also in 1982, Osaka University built what was then the world's fastest supercomputer using Z8001 microprocessors (check out the cooling system in the photo!):
http://museum.ipsj.or.jp/en/computer/other/0013.html
If you were a government agency, wouldn't you rather have a 16 MHz 32-bit 68k than a 5 MHz 8-bit 6309? Or even the 4-10 MHz 16-bit Z8001 that Osaka had used? Of course, if you were a Japanese government agency, you would have to import the 68k or Z-8001 from the USA, whereas the 6309 was made in Japan.
On the other hand, the Motorola 6809 was used for some arcade games, including Defender and Robotron. Maybe Hitachi planned to sell the 6309 to games companies? I assume that games companies controlled their entire software stack, and games always need more performance at an affordable price, so the 6309, as a 6809 but with opportunities to go faster, would have been pretty appealing. The arcade version of Double Dragon used the 6309, although five years after it came out:
Speed doesn't really matter to Liebert as its not like data center cooler thermostats are going to be typed on 10x faster by caffeinated humans or fans will spin 10x faster. Although denser code DOES mean more marketable features could be added to the firmware. Of course if you compile for the more advanced 6309 then you no longer have a second source for hardware and theoretically Hitachi could screw you over by charging a lot more than motorola charges for 6809 processors once you're dev team is stuck on the 6309. All I can say for certain is in the end, if you open a 90s era Liebert you'll see a thermostat / early-SCADA PCB with a genuine motorola 6809 on it, so that was THEIR final decision.
90s era Saturn automatic transmissions had a similar issue and they shipped with genuine motorola 68hc11 chips. Again, its not like a 10x faster processor will decrease 0-60 times by ten times, so ...
Generally Hitachi's business strategy WRT CPU licensing seems not to have worked?
But here, it's weird, especially something like division which presumably isn't cheap to implement and is useful to end users. I don't get it at all.
That Hitachi CPU however physically had those unused registers as well as that native mode where instructions wouldn't artificially be delayed to be cycle-compatible, but by default behaved like the older and slower model and was only advertised as such.
That doesn't make too much sense first glance, unless there was some glaring bug discovered after production started, or as suggested they feared it would make some more expensive "enterprisey" CPU from another lineup obsolete.