The only mode of transportation I'd call "convenient" would be flying. Turkish Airlines seems to plan more than one non-stop per day next June; things could obviously change between now and then.
There is currently no rail service between Istanbul and Sofia as far as I know. This is what the Seat61 website says at the moment:
"The Zagreb-Belgrade, Belgrade-Sofia, Bucharest-Istanbul & Sofia-Istanbul trains all remain suspended and may not run at all in 2021."
I don't believe it's safe to assume rail services useful to you will necessarily be restored quickly even if COVID somehow becomes a total non-issue early next year. Back in 2015 I ran into a group on a railroad tour on a Bucharest-Veliko Trnovo train. Two of the group's scheduled night-train trips in sleeping cars were no longer running, leaving the group with two overnight bus rides.
A bus from Istanbul to Sofia would be an all-day affair, and I'd definitely not count on the bus running on schedule every day. I've taken buses in the Balkans. It's quite an adventure. You definitely have to be prepared for eastern-style (hole-in-the-floor) toilets at the bus stations and other comfort stops. The bus driver is unlikely to speak English. The buses used on major international routes are usually comfortable, but I have no recent experience with buses into or out of Istanbul.
I'm sure there are worthwhile places to visit in European Turkey, but I've only been to Istanbul, so I can offer no suggestions. I'd suggest getting a guidebook to Turkey.
For sure Plovdiv is a very interesting Bulgarian city on the way to Sofia, but your tour goes there. Still, I think it would be worth a stop so you'd have some extra time there (Rick's tours are too fast-paced for me), especially if you have an interest in shopping for inexpensive art or crafts.
For more adventure you could also fly from Istanbul to Bucharest in Romania on Turkish Airways, or to several Romania cities on the Romanian airline TAROM. Turkish Airways gets good reviews; I have no knowledge of TAROM. Of the TAROM options my first choices for architecture would be Cluj-Napoca and Timisoara. Bucharest would be better for museums; Ceausescu wiped out a large percentage of the historic buildings in the capital. Romania is a fascinating country, very much worth a multi-week visit. I can't really recommend a quick trip there between Turkey and Bulgaria, what with the likely transportation challenges (though I imagine the trains are running between Bucharest and Sofia, albeit at a speed that definitely will not impress you).
In your shoes I'd look at eastern Turkey (realizing I might need to return to Istanbul to fly to Sofia) if I didn't turn up interesting options in southeastern Bulgaria. that would allow me to split the long bus ride with a stop or two.
You could hop over the border to northern Greece, of course, but there seem to be no trains these days, and getting from northern Greece to Sofia would be yet another adventure.
The eastern Balkans are really very different from western Europe, which makes them all the more interesting. But there are logistical challenges, so it's helpful to have a lot of time. I took two day-long bus trips to get from Sofia to Podgorica, the capital of Montenegro, back in 2015. There was some very nice scenery, but I don't think many other people would have been willing to do that. (There are connecting flights but I prefer to explore on the ground.)