The faster chip from Motorola could have been only MC88100+MC88200, which had been developed concurrently with MC68030. So Motorola really had a faster alternative at that time. Moreover, Wikipedia says that Jobs actually wanted in the beginning to design NeXT with MC88100, not with MC68030, but he gave up due to problems with price and availability.

That was a RISC CPU many times faster than MC68030+MC68882 (it had a pipelined FPU, like Intel 80860 and the much later Intel Pentium, so for number crunching it was more than an order of magnitude faster than MC68030+MC68882).

It probably was used as an accelerator, on an expansion card. NeXT had NuBus for expansion cards. I do not know if it had enough connectors for the 2 expansion cards wanted by CIA, but if any customization was done it must have consisted in providing enough NuBus connectors.

The Intel graphics could have been Intel 82720, a clone of NEC μPD7220, which could do by itself simple 2D graphics tasks (like drawing lines and arcs, filling polygons and copying the font bitmaps for rendering character strings), freeing the main CPU.

By the end of 1990, my company bought what at that time were expensive workstation variants of an IBM PC/AT clone, which had some huge monitors with higher resolution than supported by VGA, for which an expansion card with Hitachi HD63484 was used to provide really impressive graphics.

Intel 82720 was similar to Hitachi HD63484, but HD63484 was more recent and it had more features, e.g. it supported up to 4k resolution (but 4k monitors were extremely rare and expensive in 1990, so we had only monitors with 768x1024 @ 16 bit per pixel, which was still excellent for that time).

So I assume that a similar card was referred to in the article.

We used our HD63484 card only with AutoCAD, because it was the only program that had graphics drivers for it. The rest of the programs used a standard VGA card and a VGA monitor.

I assume that a similar dual monitor arrangement must have been used by CIA/NSA with NeXT, so their special application program must have used their graphics card with a big monitor, while the standard NeXT programs must have used the original NeXT graphics.