does the amount of "junk/stuff" you have stored in your workbench affect settlement size? For example, sanctuary is my "home" base, so pretty much all my junk, mods and anything else related to crafting/scrapping (like storing road leathers and such for leather) gets put in that workbench, does that have any effect on my size limit for how much i can build?

nope, you can store all the stuff you want, how it works is some locations you can build more and some you can't build as much, probably lots of factors, the city areas you can't build quite as much, open areas you can build more, so there's a limit, its quite a bit but there is still a limit, i don't max too many of them out, i build just whats necessary, jamiaca plain is a spot you can top out the max limit fairly easy depending on what you want to do, if you tear down stuff the bar will go down, so lets say you build a lot and the bar fills up, if you scrap stuff the bar starts going down, now there is a way to make the bar go down but it can cause some glitches, if you drop weapons on the ground near the workbench and scrap them, the bar goes down and you can build more, i don't do this cause i don't want a glitch, i stay within the build limit of my locations, most spots you can build a lot and won't ever have an issue, but a few of the tight, more dense locations you can max out the limit if you build a lot.