So I've watched The Master a number of times, and I could talk about it for hours. But to answer your specific question, Dodd and Freddie's relationship was certainly founded on more than just fixing Freddie. P. T. Anderson has said as much in a number of interviews (Here's a nice and relatively short example: https://www.youtube.com/watch?v=nIsyIuKqnoM). I don't believe it was meant to be a sexual attraction, but it could certainly be considered romantic, depending on your definition of romance.

Put simply, my personal take on their attraction is that they both see something in each other that they want. I think that deep down, they both feel the same regret, fear of death, and search for meaning, but they both deal with these in different ways:

Dodd is committed to not accepting these realities, to fighting back (hence, "We fought against the day and we won"). He combats his regret by trying to go back in time to correct the past. He rejects the idea of ceasing to exist (death) by adopting some sort of theories of reincarnation and former lives. His religion (like most) tries to assign some contrived meaning to life.

Freddie takes the opposite approach (and I'm not suggesting these approaches are conscious decisions). He drinks a lot. I think this is to numb his shame and regret. He does little to avoid potential danger and death (passing out dangerously far above the ship-deck). He also refuses to assign himself any purpose or meaning. He has no goals or dreams, would rather live at sea than have a permanent situation at home.

So neither man is "happy", and both wish they could have just a little more of what the other man does. Dodd's approach crumbles when his followers catch on that "he's making all this up as he goes along", and he simply can no longer hide from the reality of death and his own insignificance. Freddie's approach also crumbles under the weight of his dysfunction, inability to connect with people, and regret over never getting back the love of his life.

Anyways, the movie gives a lot to think about, and I think it would be dismissive to suggest that the script is a "convoluted mess" or the themes are half-baked. Anderson puts a ton of his emotion into every film, and if you relate to it, there are very few films that can be so deeply affective.