Actually, if we're going to get this nitpicky, the original Mac II behaved like a fully 32 bit machine under A/UX from day one (in 1988), including inside the emulated Mac environment. A/UX predates System 7 *and* Mode32 by nearly three years which makes its "compatibility box" the first example of a "32 bit clean" classic OS. Allegedly only around 10% of the existing software base would run on its weird 32-bit-only take on System 6 because so many developers had utilized the upper address bits in a 24-bit manner up to that point, so... really, from a practical standpoint it wouldn't have mattered much for the first few years if it had been 32 bit clean, no one would have gotten much use out of it.
As to why Apple never released a fix themselves in the form of a ROM upgrade, who knows, it wouldn't have been that much effort given 32 bit clean ROMs work in the SE/30 and there is little architectural difference. (The ROMs are a different form factor, of course.) Probably for the same reason they did things like not bothering to offer 64 bit updates the EFI in some of the older Intel Macs, that's just how they roll. They'd rather sell you a new one.