Were those male rats really "pregnant"?

With sophistic word games it's easy to define anything as anything. We could define inanimate incubators for early born babies as "pregnant", and that would have more merit than calling the non-pregnant male rats "pregnant" as at least inanimate incubators wouldn't be claiming the credit of someone else’s body parts while incubating babies. It's the female rat that is pregnant, putting the pregnant part of the female rat inside a male rat doesn't make the male rat pregnant, it's makes the female rat pregnant inside a male rat.

Is it even true that "males can not get pregnant", and "females can not have penises"?

It’s true that flat-chested females can get pregnant and that males can have breasts. You should just call it what is instead of using misnomers, and then there is nothing confusing or strange about it.

Males in the past have been born with uterus

Are you talking about chimeras who are the result of a male and female embryo getting fused? Anyone producing ova is by definition at least part female.

Cis men can impregnate trans men.

Human males can impregnate human females, nothing new or strange about that.

Why isn't it possible to transfer a uterus, ovary, vagina, etc to the body of a male? Why isn't it possible to transfer penis, testes, etc to the body of a female?

We can as a hypothetical imagine taking the ovaries and uterus of a brain dead female human and putting it inside a male human and imagine a pregnancy. That would be the living body parts of the brain dead female human getting pregnant inside a male human, still not the male being pregnant. A female could attach the penis of a brain dead male to her body, she still doesn’t have a penis, she is just using the penis of someone else.

If only men can have testes and penises, and if testes and penises are only male organs, why is it that women with certain intersex conditions have testes and penises?

Anyone who produces sperm (by themselves, letting the living sex organs of a brain dead male person produce it doesn’t count) is by definition male. Anyone who produces ovas (by themselves, letting the living sex organs of a brain dead female person produce it doesn’t count) is by definition female. In a hypothetical case that someone would produce both sperm and ovas (with their own sex organs, not using the living sex organs of a brain dead person) then that person would be both male and female. So either you are saying there exists males who produce sperm, and we completely agree those who produce sperm are male, or you are inventing a dilemma by incorrectly claiming we would consider sperm producers as not being male. Non-males who produce sperm don’t exist simply because anyone producing sperm is already defined as male to begin with.