Are there alternatives for booking flights unavailable directly via the airline (but available from an Online Travel Agent?)

This year I had something happen to me twice, which I never witnessed before nor I thought possible: An airline has flights for the legs that I'd like to fly on, but if I try to book the whole trip, it only proposes me a more complex trip with an extra leg. In the meanwhile, the desired booking is possible on an OTA website.

I presume that this might be because OTAs have access to more inventory, but this seems weird. The two examples were:

London to Yekaterinburg: I flew with British Airways + S7. They are partner airlines and S7 can sell me the London-Moscow leg of the trip, but S7 was only offering me a more complex trip (something like: London - Berlin - Moscow - Yekaterinburg)

London to Longyearbyen: I booked a SAS trip with Layover in Oslo (cancelled due to Covid19), but the SAS website was only offering me trips like: London - Copenhagen - Oslo - Longyearbyen or London - Stockholm - Oslo -Longyearbyen

In the above cases, I booked from an OTA, but I'd really prefer to avoid in the future (in one direction, my luggage couldn't be checked-in all the way through even if that went smoothly on the way back. I got multiple check-in codes for the same booking, and making changes is just overall much more painful if a travel agent is involved).

I just managed to find another example (again, for Longyearbyen: just an example, since I'm not currently planning of flying there in September):

As you can see, for the day only trips with 2 layover are offered.

But I checked on 4 different OTAs, and all of them are offering a booking with a single layover:

• Expedia

• Lucky2go

• Lastminute

• Gotogate

This seems even weirder, when you consider that the single legs are actually available for purchase on SAS itself:

But somehow, SAS doesn't allow me to purchase this trip directly with them.

How common is this? Are there other solutions besides booking via an OTA? Would I be able to maybe get the booking done by directly calling the airline? (and if so, would this be standard practice, or should I expect it to be hit and miss depending on the airline?)