After receiving several suggestions to use a bigger board, I acquired an economic S7 regular ATX board: the Gigabyte GA-586STX2. (SIS 5582 chipset)
The board unfortunately has one problem: the 1.0 USB is dead as far as I can tell. I also noted that it didn't work well with Sata SSDs via IDE converter. Not sure why, but not an issue really as I have enough CF cards.
In order to use the board with CF cards in Win98se DMA mode, I need to disable ultraDMA in bios. I found the suggestion in this forum, as others encountered similar DMA problems before.
The board offers 3x ISA and 4x PCI unshared. So there is plenty of room to use. Please note this isn't SS7, FSB can be set to max 75 MHz. No AGP. 32GB HDD support.

I have run through most of the decision making by now and would hence ask for some general feedback on the following plan:

Purpose:
1.) To use mmx slowdown methods to cover as much DOS as possible. The idea is to be able to deal with DOS games from the 90s, including the speed sensitive ones.
2.) To cover the early 3D era with 3dfx DOS and windows games.

PCI cards:
ATI Rage II+DVD, 4MB, pci. I have seen it has some issues with a few DOS games in the compatibility matrix. (decided against the Riva128 for now, as the ATI stays much cooler and 3D will be provided by Monster 3D, can always swap later)
Diamond Monster 3D pci (enough heat for two cards) (Might be inserted on demand only)
Nec USB2.0 4+1 (to avoid permanent slowdown, no internal card reader will be used)
free slot for rear CF-IDE adapter.

ISA cards:
ESS 1868F card with add on wavetable Nec XR385. Set as A220 I5 D1 P330 T4. Has the job to act as soundblaster pro clone with midi board. (I compared the sound to yamaha-719, but overall prefer the somewhat darker timbre/filtering).
Soundblaster AWE64 CT4380 value (512kB). Set as A240 I7 D3 H5 P300 E640, FM disabled. AWE64 does the SB 16 job and provides AWE32 when supported. I could swap for 64gold if the ram would make a difference. The gold is otherwise employed in a P2/P3 machine.

Ram: 64MB
CPU: Pentium MMX-233 (or dip switched to less)
HDD: various CF-cards.
DVD: some IDE burner that does spin down quickly.
Disks: 3.5" floppy drive
Case: Small black ATX case, 1x 5.25, 1x 3.5
OS: Win98se