The Colonel is Charlie's father - I know I cannot be the only person who thinks this.

I think that would be too "neat". The coincidence of it would make me just roll my eyes. Other films have done similar things (often it's trying to connect villains to heroes through unlikely familial connections) and I almost always hate it. Sometimes it's done artfully (although I can't think of any (literally none) off the top of my head). Most of the time, it's a big miss.

For my money, I don't think Frank is Charlie's literal father, but by the end of the film, he kinda is.

Not at all. Charlie is just someone his family hired to watch over him while they get away for the weekend.

There’s absolutely nothing to support his absurd theory, and Frank even asks Charlie where his father is.

Next time pay attention to the film before positing such mindless guff.