At the time it made more sense to still produce the old-style keyboard since they were making two lower-end models that used it.
This is supposition, unless you have access to something that details this. Certainly that
could have been the case. At some point Apple did do some consolidating by only offering the Plus keyboard with the 512Ke. However, from a marketing perspective, Apple could have eliminated the pre-packaged Plus keyboard, dropped the price and offered the customer a choice of the new hybrid keyboards, ultimately resulting in a higher profit for Apple. Remember Apple was a volume company and despite the enormous profits they were reaping in the late 80s, they continued to strive to shave a penny from a 10-cent part, which would result in a net profit of $10,000 over a million units without changing the price. So eliminating an entire keyboard would have had a substantial result, especially over 3 years (no matter how much profit they were already making on it).
What always puzzled me was why the IIGS keyboard couldn't have been used as the regular-length option on the SE. Sure, it worked, but was the designing of the Apple Keyboard (the short model most people bought with SEs) really necessary?
Paul Kunkel's Apple Design makes that quite clear. Hartmut Esslinger pushed for the IIGS keyboard design, originally without the thin border surrounding the keys like the recent white Apple Keyboard. However, Apple made him add the border because they felt the keyboard looked flimsy. When the SE & II came out, they wanted keyboards that looked sturdy and business oriented (the IIGS was a "hobbiest computer" for gaming, so it didn't matter). Esslinger was on the way out at that point so they redesigned the keyboards, which also helped them boost profit – who would pay a premium for something Apple felt looked flimsy? A whole different mindset then than today – they were competing with the typewriter and the computer had still not replaced it for a majority of businesses. I don't think the IIGS keyboard was ever officially sold separately, which is too bad because it looks best with the SE. Again, if Apple did replace it with the Apple Standard Keyboard, there is evidence of consolidation to maximize profit.