So I may have fixed the issue noticed here.
TLDR: The NuXT is not failing to boot. It is failing to print to the screen in monochrome mode. You can still enter commands, you just can't see what you are typing. Two bugs are at play here. The Trident 9000i randomly boots into Monochrome mode, and the 8088 BIOS stomps over parts of the VGA BIOS Init. I can't fix the former, as it's a hardware issue. I believe I fixed the latter.
Long Version: The VGA BIOS of the Trident 9000i sets bits 4 and 5 for "Initial Video Mode" when it's initialization function at c000:0003 is called. It then looks at those bits in it's IRQ 10 handler to decide whether it's working in the address space b000 or b800. If "Initial Video Mode" is 3, it works in the b000 address space, writing characters and scrolling memory there. Otherwise it works in the b800 address space.
The 8088 BIOS the NuXT is running initializes the VGA BIOS, then immediately sets those bits to 0. Which makes a certain sense, going by a lot of the extant online documentation I can find. Most of them say 00 means EGA or later, with not much more to say on the matter. Either the Trident BIOS is doing something really nonstandard, or the intent of these bits is not to say what physical hardware is installed, but what the initial/current display mode capabilities are. Either 40x25 color text, 80x25 color text, 80x25 monochrome text, or some EGA/VGA display mode. A VGA card booting into 80x25 color should still set the bits for 80x25 color, not 00 for EGA+.
Or at least that's how the Trident BIOS is treating it. I may have dumped the ROM from my NuXT, fed it through a disassembler, and stepped through it's initialization and print functions to see where and why it was going off the rails in monochrome mode on the NuXT. Sent a pull request up through github, just commenting out the line which wipes those bits after VGA initialization. The fix works on my NuXT, but I'm not sure how other EGA/VGA cards might react to that change, since I have none to test it against.
What compounds this bug in the BIOS is that the Trident 9000i seems to erratically boot into monochrome mode when connected with a "modern" monitor. I saw posts online describing this happening going from a 1994 vintage CRT to a 1997 vintage CRT. The evolving usage of the ID pins just confuse it. So these two bugs together make it seem like the NuXT occasionally fails to boot.
Win95/DOS 7.1 - P233 MMX (@2.5 x 100 FSB), Diamond Viper V330 AGP, SB16 CT2800
Win98 - K6-2+ 500, GF2 MX, SB AWE 64 CT4500, SBLive CT4780
Win98 - Pentium III 1000, GF2 GTS, SBLive CT4760
WinXP - Athlon 64 3200+, GF 7800 GS, Audigy 2 ZS