so was Homelander actually telling the truth?

In his mind. Her's we don't know.

Since the video of her gettin out from Homelander office i suspect could be consensual she was to calm, some people would say some rape victim are too much in shock to show any emotion inmediatly and to those i would respond this is a fictional history and everything that is show to us is product of a creative and narrative decision from the director and screenwritter in that scene the director at least put the seed of the doubt in us about what could happen in there, and dont forget Homelander say "she cum 3 times" and in any moment he talk about it like was a rapped and this guy is a monster but he knows what he is doing he just dont give a f so i dont think he is delusional about what happen in that office with butcher wife was conssensual

pretty sure it was consensual.
the moment billy tells the story, i was like, how the hell he know he raped her? was he watching bye and lived afterwards?
if something this shows established is not everybody is one dimensional good or bad, so i had that thought, what if she just desired some hero D?
so i was not surpised no rape was shown on the video footage
she just left the office, a bit shaken, but who wouldn't after riding superhero D for 3 hours? :)

it was billy who made it rape, because he assumed she loves him deeply,she has got be forced to this.

and finally the biggest reveal was simply at the end.
when they met becca's reaction was totally not like:" oh no the man who raped me and ruined my life"
it was more like: o"h oh, im going to have some serious explanation to tell these guys"

I would think that yes, it was - at least based on what we saw on screen.

If there would have been a rape would have been either shorter either HL would have left first the office.

And her reaction at the end was quite expressive, she was smiling at HL and gave a "wtf" look at Billy.

Well i mean i doubt it was a situation where he just grabbed her and raped her while she was yelling and fighting, she was likely very afraid of him and consented to it even though she was not into it. So i think she consented to it and in Homelander's eyes it was consensual, but she only consented to it out of fear. So it was still rape.

And as for her looking happy to see Homelander and not Billy at the end, Homelander could kill her at any moment if she made him mad enough its no surprise she acts glad to see him. She likely really hates his guts but can't let him know it out of fear.

100% consensual as there was no rape warning like in the first episode.

I don't think it looks like Becca was crazy about Highlander and she didn't really seem like the type to go gaga over him either..
She seemed shellshocked coming out of that room ....so I'm going to go with she was coerced but Highlanders ego would never see it that way.

She disappeared to protect Butcher and to protect the child from Highlander and the whole crazy corporation..

I think it was consensual. Reason being is his interaction with Stillwell. In both encounters with her, he was almost like a submissive boy. He showed no tendency to be sexually aggressive or dominant. Dude is crazy, but I think he may have sexual insecurities. Just a guess.

And actually, I think Becca came on to him first.