Thanks Josh,
It looks like your implementation makes the scroll bar work, but sadly it also causes the text to be located in a strange place, and the border to be larger than I want it to be. The scrolling by a page issue isn’t a huge problem for me though 
I’ve done some work on styling using your advice, and I’ve got something which is very close to what I’m looking for, but it doesn’t yet respond to window resizing like the rest of the passage:
#bottom-container {
position: fixed;
height: 6.5em;
bottom: 0em;
left: 0;
right: 0;
z-index: 20;
background-color: #ddd;
}
#bottom-wrapper {
margin-right: 2em;
margin-left: 19.5em;
}
#bottom {
max-width: 864px;
margin: 0 auto;
border-top: 1px solid #333;
padding-top: 1em;
padding-left: .5em;
padding-right: .5em;
}
With the following formatting applied to passages, so that any text hidden by the bar can be seen when you scroll all the way to the bottom:
body.options #passages {
margin-bottom: 5.5em
}
The reason for all of the wrappers is so the bar works like the rest of the passage. The padding causes the bar to be a little bigger than the text which gives a nice effect. I saw that TheMadExile formatted a bar with similar resizing functionality here: https://twinery.org/forum/discussion/2328/how-to-push-text-to-the-bottom-of-the-page and I’m going to attempt to copy the fancy formatting that they used.
If I were more adept at formatting I would also try to make it so the height of the bar is dependent on the height of the text contained within it. I think it would be difficult to make the margin-bottom for the whole passage react to the height of the content of the bar though.
EDIT:
Thanks to TheMadExile’s code, and some use of the chrome “inspect” tool, I’ve managed to achieve the desired results, barring the variable height.
I’ve added the formatting for window resizing:
@media screen and (max-width: 1136px) {
#bottom-wrapper {
margin-left: 18.5em;
margin-right: 1em;
}
}
@media screen and (max-width: 768px) {
#bottom-wrapper {
margin-left: 3em;
}
}
With the formatting for the stowed bar:
#ui-bar.stowed~#story #bottom-wrapper{
margin-left: 3em;
}
I also have changed added a transition which makes the size adjustments smooth, matching the story passage formatting:
#bottom-wrapper {
margin-right: 2em;
margin-left: 19.5em;
transition: margin-left .2s ease-in;
}