I won't speak to the heritage side of this, but only the logistics. [For reference I am a white American woman who knows only like 200 Urdu words]

The sites are definitely worth going to if you are in Karachi for more than a few days and it's a shame that more people do not go. Makli is only about 1.5 hours away from the city. Not extremely well-kept which is a shame, so worth seeing now before any more damage occurs. The necropolis itself is very large, so you can hire a long golf cart for 100 rupees per person at the entrance. Foreigners must show passport and visa at several stages. Chaukundi tombs can be seen on the way there, and Shah Jehan mosque in Thatta afterwards. When I was there, we were the only ones at the Chaukundi tombs (which are an extension of the Makli necropolis) except for the guards/caretakers. One man told us a lot of history there and details of the tombs. He was very knowledgeable and friendly and we tipped him upon leaving. At Makli, inside and outside the entrance has some beggars so it is advised to move quickly once exiting your car and you can enter the golf cart. Was disappointed to see a lot of trash outside of all of the sites, due to the corrupt nature of the Pakistani government in appropriating UNESCO funds.

The road from Karachi to Thatta is safe for a day trip, and well-kept. As of May 2023 they were doing some construction on the Karachi-bound lane and forced both directions of traffic into the other lane without any safety cones, etc that you would see in developed countries. But just make sure you have a good driver and you'll be fine. For non-Pakistanis, I would recommend going in a larger van group with a driver or with privacy screens on the back windows of a car just to avoid any attention.

There are also other archaeological sites on the way and towns, including the Bhanbore site and town of Gharo (stop to eat at Cafe Imran and get the chicken karahi). I went with Humsafar Tourism who organized the trip quickly for me.

All in all, an excellent cultural site to visit in Pakistan that's very convenient to Karachi. Don't expect western-level amenities, but the food along the way will be astounding, and the sites and history unparalleled.