Middle East - Transiting IST?

There was an oooold thread but I was wondering if anyone has experience lately...

A post in the CO forum regarding the wide open R (upgrade) space on the new EWR-IST flight yields the intriguing possibility of having a decent way to get 90% of the way to TLV from EWR (given that EWR-TLV is the hardest upgrade in the system, this is super nice).

I found TK has flights that have a long connection (5h) outbound, and <2h returning. If the short connection doesn't work there is a super-sucky 5:50a flight....

The 5h connection shouldn't be a problem; but
A) is it possible to check into TK from the "transit" zone; and
B) would it be (possible) to check into the UA flight either in TLV or in the transit zone.

Yes, they have a transit desk in the transit zone where you can check-in and obtain your boarding pass. (In fact, there is a separate counter for high-security destinations including the U.S., U.K., and Israel, where lines are long sometimes, but two hours should be enough.)