I had this same problem. After a bit of research I found out that the TOP series of programmers doesn't play well with 48 pin TSOP chips (and some other 48 pin chips). I ended up making an adapter that shifts the pinout by 13 places, allowing you to program any previously unsupported chip. The adapter can be used to directly program any 48 pin TSOP on any TOP programmer, OR allow you to plug in your existing tsop48 adapter or 48 pin chip.
Writeup:
https://blog.kenzycarey.com/2020/07/programming-48pin-chip-with-top.html
Store:
https://www.lovegood.dev/2020/07/top-48tsopdip-adapter.html
eBay:
https://www.ebay.com/itm/233638652572
I purchased ebay adapters for tsop48 to dip 48 and each time I loaded a 29400TA-12PTFN [I selected AM29F400T_(TSOP4

] as the chip type it would error out with this..
I then came across this post - like you after searching and searching..
https://www.mcumall.com/forum/topic.asp?TOPIC_ID=2604
This was the part that was of great interest
So I rigged my converter up to the way the post had, dip pin 1 goes to tsop48 pin 13 onwards.
When I tried to burn the flash, it would appear to have burnt it, but each time I tried verifying, it would error out. Needless to say, I still tried soldering the flash back on to the cart, but all I got was a suicided cart - it may have been my soldering job, but I went through it with a fine tooth comb and could not find any issue with my soldering.
I've now just purchased one of your adapters hoping to have my CPS3 bios woes sorted with this. I am assuming I can also burn naomi flash with this adapter?
Finally, when flashing 29F400 roms, is there a particular one you're choosing from the options? And are you just loading up Darksofts file and then "writing" no special options?