Those experienced with designing bodyshells have lots of tricks they can use. One of the ways you manage panel gaps is to design the vehicle so that the gaps don't matter where possible (e.g. the edge of the panel comes up to something that inherently has a big opening or mismatch or is covered by a trim piece, as opposed to an adjacent panel whose edge has to coincide). Another way is to arrange to only have to align a gap to one adjacent part as opposed to having to match a gap on multiple sides of the part to multiple other parts. A big factor is how you manage your tolerance stack-up. Another big one is to take designed-in flex into account - the door gap has to be correct when the door is fully assembled with the interior trim and window glass and insulation etc, not necessarily when it's still an empty shell.
I drive a cheap little car built by a collaboration with two manufacturers that "the common wisdom" suggests they don't build quality products: Fiat, and Chrysler. Guess what ... Panel fitment is pretty good for what it is. And it has plenty of examples of designing such that the gaps don't matter as much. There is a skirt on the rocker panel that extends out from the bottom of the doors ... this also means that the edge of the door doesn't have to match in the in-and-out direction because the piece below it is at an angle anyhow. Likewise with where the trunk lid is adjacent to the rear bumper skin, which sticks out a bit past, so the alignment isn't as critical (lots of cars are like this). Likewise, the front bumper skin / fascia (which is one great big part) projects out past where the hood closes next to it - it's a design feature of the styling, but it also means it doesn't matter if the front edge of the hood is fore or aft a bit. The side / bottom edge of the hood also coincides with a design feature on the fenders, a crease that extends out a bit (and goes all the way around the car). Result ... if the side/bottom edge of the hood is in or out a bit, or if the fender itself is in or out a bit, you won't see it because the gap coincides with an angle between the two parts anyhow.
I drive a cheap little car built by a collaboration with two manufacturers that "the common wisdom" suggests they don't build quality products: Fiat, and Chrysler. Guess what ... Panel fitment is pretty good for what it is. And it has plenty of examples of designing such that the gaps don't matter as much. There is a skirt on the rocker panel that extends out from the bottom of the doors ... this also means that the edge of the door doesn't have to match in the in-and-out direction because the piece below it is at an angle anyhow. Likewise with where the trunk lid is adjacent to the rear bumper skin, which sticks out a bit past, so the alignment isn't as critical (lots of cars are like this). Likewise, the front bumper skin / fascia (which is one great big part) projects out past where the hood closes next to it - it's a design feature of the styling, but it also means it doesn't matter if the front edge of the hood is fore or aft a bit. The side / bottom edge of the hood also coincides with a design feature on the fenders, a crease that extends out a bit (and goes all the way around the car). Result ... if the side/bottom edge of the hood is in or out a bit, or if the fender itself is in or out a bit, you won't see it because the gap coincides with an angle between the two parts anyhow.