乗り継ぎ保証はないと思いますが多分可能ではないかと思います

長いタイトルですが、
空港サイトのFrequently Asked Questionsを読むと。

How much time ahead is needed for boarding the aircraft on time?

The time required depends upon the destination you are flying to. For domestic flights the time required is 90 minutes, whereas you should allow for 120 minutes for international flights. For any additional information please refer to web site under section: Passenger Information.

Is it possible to have a fast passport control or luggage registration from one flight to another?

Minimum connecting time at Zagreb Airport is 40 minutes. In case Your luggage will be correctly through-checked from Your initial departing destinaton - all the way to Your final destination, all that You have to do on arrival at Zagreb Airport is to pick up the boarding pass for your next flight at the transfer desk located in the International arrival (BEFORE You go to the passport control). Our airport is not a big one, there are no long distances and everything is groundfloor, so 1,5 hours will be quite enough to transfer from one flight to another.

We fly from Amsterdam to Zagreb and from there to Split. Scheduled arrival in Zagreb 13.10 hrs, departure to Split 14.30 hrs. That leaves 80 minutes for transfer. Can we make the connecting flight in time?

Minimum connecting time at Zagreb Airport is 40 minutes. Our passenger terminal is not the big one, there are no long distances and it is all groundfloor. At Amsterdam Airport check-in staff can through-check Your luggage to the final destination Split and give You a boarding pass for that flight. That will make Your travelling much easier and Your connecting time (arround 80 min) will be more than enough to transfer from one flight to another.

とくに、別に同じエアラインとも書かれていないし、同一予約でないとダメとも
書かれていません。

ただし、予約が異なれば、MCTをクリアーしていようがいまいが関係ないのも
この世の常。

オープンジョーですが、オンライン予約で対応しているほうが少ないと思います。
国内が全く同じ料金なら、代理店経由とか、エアラインに問い合わせる、または
片道x2=往復ならば、問題ないし。