OK, I finally have time to report back on my experience in mid December.

I flew into KRT on Fly Dubai from DXB as it was a cheap flight and I had flown ex-US to AUH on Etihad (using AA miles; EY released an F seat about 3 days prior to flight, so I switched from a previously booked RJ flight via AMM; nice complimentary limo from AUH to Dubai.)
I had arranged an airport entry permit through Waleed, but agent at DXB did not ask to see any evidence of visa for Sudan.

On arrival at KRT, it took about 20 minutes for visa to be processed as they shuffled my passport and forms around a couple of (open) offices.

I stayed four nights in Khartoum; interesting but probably only needs two or three nights to see the few sights.

Departing to start my RTW: it's fortunately only about ten minutes from the centre of the city to the airport and little traffic at that time of morning for the 06.25 RJ flight to AMM.
You cannot check-in online for RJ flights from KRT.
Check-in is handled by contract agents, not RJ, and there is little organisation, no signs, and no J class lane. I asked a porter if there was a check-in area for J and he told me just to go to the front, which I rather reluctantly did and asked the check-in agent where J passengers check in, and he stopped what he was doing and took my passport and checked me in! No premium baggage tags available, and my suitcase was automatically checked through to DEL.
No queue at Immigration counter, and I asked two different Immigration agents if you can do Transit Without Visa if arriving on RJ and departing on same plane, and both said it would be fine, though they couldn't understand why I would want to do it, and were more concerned that I wouldn't have enough time to meet whomever I was planning to meet at the airport for business!

There's no shopping after Immigration except a small souvenir stall, but there's a small contract J lounge before security with sandwiches, salad and hot & cold soft drinks. An agent calls for Y passengers first, and later calls for J passengers who go on the last bus to the aircraft.

At AMM, I went to transfer desk, not sure if I would clear immigration or stay in the airport as my DEL flight didn't depart until 21.15, exactly 12 hours later. Staff at transfer desk immediately escorted me to "airport hotel" desk next door, who then escorted me through Immigration without needing a visa, and then to the terminal exit where a small minibus was waiting to take me to the Golden Tulip airport hotel, about ten minutes away on the airport access road. The driver told me not to take the regular shuttle back to the airport, but that this minibus would be waiting for me two hours prior to my flight.
At the hotel, they gave me a very comfortable room, and provided lunch and soft drinks, all at no charge! I hadn't expected that. And indeed the private minibus was waiting for me at 19.15

The minibus dropped me at the dedicated J class check-in lounge, and I again asked the check-in agent about doing TWOV on the inbound and outbound flights. (I am hoping to do this in April when my DONE4 ends and I start an AONE3). He confirmed that it would be OK, but that they cannot check me in at AMM for the KRT-AMM return, but that he would send an email to their station manager at KRT who would print my boarding pass and meet me on arrival at KRT.

Sorry this is a bit long, but I hope the info may be useful to others.

Happy Travels.