I see. I assumed that PAE was mainly activated here in order to be able to use DEP or NX-Bit.
In essence, DEP tries fix the biggest flaw of that overrated flat-mode, the possibility of executing code in data.
In the old 16-Bit/80286 Protected Mode, there was memory-protection based on segmentation.
In theory, this feature is still available, but modern OSes nolonger use segmentation, sadly.
When developers moved to 32-Bit programming, the 80386 MMU (in 32-Bit Protected Mode) was usually instructed to inflate the segment size to 4GB, thus essentially making the segmentation-unit inoperable.
DEP tries to fix this my making certain code/data block in flat-memory non-executable.
If segmentation was still in use, the 4 GB barrier wouldn't exist in first place, also.
Physical memory might be still limited to 4GB, but virtual memory size (segmented) would be 1GB for 80286, 64TB for 80386+.
Edit: Another excuse by MS was that NTVDM depends on V86 and that V86 can't be used in x64 long mode.
Which in turn is merely true in part. NTVDM existed as pure emulator, too, for example.
Then, x64 long mode still permits execution of 16-Bit Protected Mode code, which most Windows 3.x applications use kind of.
Thing is, there's no real difference between Real-Mode and 16-Bit Protected Mode code if the default segment size of 64KB is used and no memory arithmetic is done.
That's why many Win16 programs run fine in different kernal modes of Windows 3.0 (Real-Mode and 16/32-Bit Protected Mode; 32-Bit PM with V86 additionally enabled).
The 16-Bit code in those applications merely does perform API calls to Windows (and DOS/int21h), it's not manipulating memory addresses (that's something Windows 1/2 applications sometimes did).
So it would be possible to run Windows 3 programs directly in x64 long mode, too, if a custom WoW was made for a non-V86 version of NTVDM:
Concurrent DOS had the ability to multi-task well-behaved DOS applications on a 80286, for example.
So if MS-DOS 5 (the core system) was modified to run in 16-Bit Protected-Mode VM,
it could host a modified Windows 3 with a modified 16-Bit Protected-Mode kernal that's x64 long mode friendly.
But even if a full-fledged emulator was used in 64-Bit Windows, performance would still be fine, because it would still be way past a 286/386/486 performance level.
Edit: I'm too chatty again. I'm sorry.
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