You will ONLY get a free TK transit hotel if you book No. 1.
No 2 og 3 are not shortest possible connection time at IST because there is an earlier flight to GVA. Most likely you will be denied a transit hotel when you turn up at the TK hotel desk, BUT there has been a few reports that also for a later same day flight to the Euopean destination, a transit hotel has been granted when the shortest possible connection is still 12 hours or more, but I wouldn't count on it (TK staff are known very much to play by the rules, and strictly speaking you are not eligible).

OTA booking is irrelevant. Done that before without issue.