I understand where you're coming from, so I'll answer the question as best I can, and hopefully anyone else wondering the same thing can simply be redirected to this response in future.
I'd like to start by tackling your claim that the harem and romance tags are odd. Whether you start at 0 work you're way up to 100, then start back at 0 and work your way up again, the game still has both romance and harem to it. Just because it's a different harem in each part doesn't make it any less of a harem.
Next, your question if Part 1 is pointless. The simple answer is no. Captain, you, learn and grow from your experiences in Part 1, and while you are forced to leave, I never claimed that that would be the last you saw of those characters. I know the choice to do something like this is odd, but I'll explain it in the next point. Right now my focus is simply writing a good story that will invoke a myriad of emotions and hopefully leave its mark as something that could move you. The relationships do matter, as even in Part 2 Captain will remark on or think back to these.
Lastly, why the weird format and what's my plan. I'm truly grateful for everyone who supports me and this game, but for projects like this that are typically low to no profit the most important thing is self-motivation. Projects that are simply "here's a new girl to romance" every time a character's story pr growth is complete would not keep me motivated. My approach is more... like a series of books. A sequential series of intense stories leading to an explosive finale! The constants in this case are Captain and the main trio(Kiana, Mei, Bronya), albeit different versions of the latter. I understand my approach is very atypical, but without saying too much, players will soon come to understand that while Part 1 and 2 are seemingly separate entities, they are very much tied together. My goal is for each part to feel like a different game, while still holding its core values, hence Part 1 being a typical Visual Novel, and Part 2 being a bit more sandboxy with an element of combat.
I hope this answer satisfies you and any other player wondering the same thing. If you do decide to try it out I hope you enjoy it, and feel free to leave any constructive criticisms, preferably on the Discord as I'm on F95 maybe once or twice a month.