While frustrating, the reason behind it is actually quite cool. For performance reasons, the TF2 level compiler automatically breaks each area of the level into "visleafs", or visible chunks of the level. As it compiles, it determines which visleafs can be seen by other visleafs throughout the level, so at runtime only the areas that are already determined to be visible will render. If you've ever thought that TF2 levels tend to be kind of maze-like, it might be because they're made that way on purpose. By creating areas of the map that aren't possible to be seen in other parts (around a corner, behind a wall, etc), the CPU doesn't have to work as hard while you're playing the game, resulting in better performance.
The problem that I ran into was my awareness of how visleafs are created. Hammer automatically divides the level up into probable chunks based on how solid, vision-blocking objects were placed. If everything in your level is a solid, vision-blocking object (which mine were), the divisions of the level will be quite small, quite ugly, and quite numerous. So numerous that it would practically crash your reasonably well-spec'd computer.
Fortunately, it's possible for me to retroactively go back and change the properties of my world-objects. The layout of my level was pretty open to begin with, which might have poorer performance because many places on the map have to draw almost the entire level. I'm hoping that the small size will make up for this oversight.
Here are some pictures of the level I've been working on, pre-detailed. I've spent around 25 hours reading up on Hammer and creating the level, and I look forward to fixing some of the necessary changes next week.
Overview of the map
Early roof work
View from the lower level of the map
Inside one of the flag rooms. The third entrance is just behind the camera.