How can I create custom navigation below the slide in Storyline?

The dimensions are going to be wonky regardless and you just need to choose where to take the L. If for instance the final product will export to widescreen 16:9 and if you wanted to have the footer stretch the entire width, then whatever content you show above it will need to be of different dimensions. If you want to show a video above the footer and the video is 16:9, scaling the video down in a 16:9 project so that the video's full height can be see with the footer will leave black bars on the sides of the video.

Conversely, if the footer were perfected already, any videos could be edited to fill the non-standard dimensions created by the foot. The videos would be non-standard, but when taken as a complement to the footer, the effect to the learner would be of a full-screen experience.

I'm a big fan of animating elements on the screen to resemble video while it just actually being an eLearning, so for me I'd design all future content for this project with the understanding I'd be aiming for non-standard dimensions.

I wouldn't try changing the dimensions of the project to anything non-standard either. I can understand the thinking of "1920x1080 plus a 300-pixel footer means the video dimensions should be 1920x1380, but then the final published course will be taller than the average monitor and create black bars on the sides of the whole course instead of just the video.

Are you sure you need the footer to be underneath certain content? If you put it on a slide layer of a master slide, the footer can always appear on time of any content for easy access. Just add a trigger to the master slide to show the layer when the timeline starts.