One 5 minute mp4 file I had, I cut a minute off with kdenlive and the resulting mp4 file was nearly twice as large.

What was the bitrate of your footage and what was the bitrate of your render profile?

I'll ensure that the bitrates match in future, is there any options to decrease the size of the file?

Well, my post has not been meant as an advice, but as a hint. The one should be approx. twice the other.

But if you make the bitrates match, you will notice that the file size of the new file will be smaller.

High bitrate -> larger file
Low bitrate -> smaller file

That's all.

To put it more exactly,

file size = (video bitrate + audio bitrate) * duration / 8

with some small deviations, as the requested bitrate is more a hint to the encoder than a strict order, and there will be some headers and other stuff.