No Stupid Questions

The female reproductive organs are actually quite small, they take up very little space at all unless there's a baby in them, and clearly we can see what happens then. Your heart is on the order of 300-400 cubic centimeters for example, while the uterus is usually about 50-100 depending on certain factors. Ovaries are like 6-7 cubic centimeters each. The vagina is collapsed unless occupied, so takes very little space as well.

Men have a couple of replacement pieces (like the seminal vesicles) but they're tiny.

The vast majority of that area in both genders is taken up by things like the bladder, parts of the colon and rectum, muscles, and fat.

Apparently my prostate.

Roughly, the same originating cells in utero become both sets of genitals and reproductive organs.

So, since the uterus isn't there, nothing is taking up that space. That space simply doesn't exist.

Yes, women have a perineum. The labia and vaginal entry take up approximately the same space as the scrotum.

Look, this is really complicated, but the over-simplified version is that, on a cellular level the tissue for one set of crotch bits is roughly homologous in both sexes. They just develop different shapes based on developmental signals. A full surgical transition usually involves taking bits from the original equipment and grafting it in such a way that it forms the opposite set of equipment. in M-F they usually go as far as reconstructing a vaginal canal and no further, because a uterus and the rest are complicated structures to create. Technically vestigial tissue for both types of gonads generally remain in both sexes, so it theoretically could be possible to synthetically create a full uterus, ovaries and Fallopian tubes and all, but the ability to synthesize organs of that complexity is currently beyond our technological capability. Functionally you're left with the equivalent of what a woman would have after a hysterectomy (eg. for something like ovarian or cervical cancer).

And yes, they still have a perineum.

Now I'm no expert but clearly there is still space in there cause that's how "stuffing" works.

the testicles are homologous to the ovaries, without the anti-mullerian hormone, the male will develop into female parts despite still being male. there are a few syndromes, genetic conditions that will do this , its rare though. like swyer syndrome. but it wouldnt be functional because it still need the female genes and their chromosones to make the uterus, breasts,,,,etc. it gets complicated if you delve into how sperm and egg gene expression occurs.

The female pelvis is wider than the male pelvis, so it creates more space for that 'indoor plumbing'. In both a man's and a woman's pelvis you'll find intestines, a bladder and muscle/connective tissue. A woman also has her uterus, overies and upper vagina. A man's pelvis includes some seminal vesicles and prostate.

And yes, a woman does have a perineum.

Human anatomy is pretty cool, but I don't know if this answer can be condensed neatly here.

Human Reproductive Biology by Kristin H. Lopez and Richard E. Jones is said to give a good breakdown on this.

The Reproductive System at a Glance by Linda J. Heffner, Danny J. Schust can also provide good detail with visuals.

The prostate and seminal vesicles take up space in that area. They are generally just a smidge smaller than a uterus and associated stuff. Women also have slightly wider pelvises than men. So it's really not as big of a difference as you'd think.

Courage, or ego, depending on varous complex genetic factors.