Finally got it working:
1) Upgraded BIOS to 306
2) Loaded default BIOS setting to CMOS (according to bios upgrade instructions)
3) Moved Realtek network card to PCI slot #2. I guess the first slot is reserved for graphic card. It just does not work there.
XT-IDE started to work and large hard drives are detected. CDROM is detected in MS-DOS and FreeDOS, not in BIOS (that's normal).
But FreeDOS installation on 486 has some bug! Lack of runtime memory or some cache. It took 3 hours to figure this out. It tells something about cannot read file from CD or cannot write file to HDD. I googled some person had same problem and solved it by installing FreeDOS on Pentium, then moving the drive back to 486. And that's what I did and that's the only solution that did work for me.
So right now even CompactFlash IDE is finally detected. FlashFloppy USB emulator working as well. I'm getting happy where this is going 😀
Replaced old NEC CD drive (probably 4x speed) with modern LG DVD drive and even the CD-RW FreeDOS LiveCD is faster now.
Next thing will be probably bigger CompactFlash card or SATA to IDE bidirectional adapter for SSD to get rid of moveable parts and install original CD-ROM games easily. Also need to discover the Samba FreeDOS networking and perhaps VNCViewer or WWW browser in FreeDOS.
Now I'm waiting for my PC AT to USB Teensy smart converter with USB HID support to connect a modern mechanical USB keyboard on this 486.
That TSENG 4000/w32 in ISA slot have much nicer colours (even not VLB) than S3 Trios64V2 in PCI. That S3 has too much brightness, the black screen in boot menu is gray. Interesting. Bought 486 for 300 Eur, spending 200 Eur more on it and still not done 😀