Gowdy didn't pitch in a game during that span, so if the problem wasn't TJ from the start, then when did the injury occur. Given how little he has pitched for us, it wouldn't surprise me if he was pitching through discomfort/pain from the start and has been injured from the day we drafted him. Likely the injury grew worse over time, but pitchers have pitched for months with elbow woes, before something completely snaps or they are just unable to continue.
Any way you slice it, this makes it a lot harder for Gowdy to reach the Phillies' rotation. 2019 is a recovery from injury season, then the Rule 5 decision must be made after 2020. If he is as good as Hamels was, although Hamels didn't lose this much time to injury, then he'll be ok.
And to be totally accurate, let's not ask specifically "how did a stiff neck turn into biceps tendonitis, turn into TJ surgery." The unambiguously accurate statement is: how did a shutdown, which was described in press releases as a stiff neck, turn into new press releases of biceps tendonitis, with an announcement of a late July/early August return, which turned into a press release that TJ had already been performed by a non-Phillies doctor at a time that the need for surgery had never even been whispered, apart from posts on this board, which were nothing more than rampant speculation -- at least I know my mention was nothing more than that.