I've had making it possible to make a random point on the minimap your destination on my todo list for a while but it isn't high priority. I'm probably not going to mark every bookmark that the player has on the minimap but I'll think about what would be nice there.
The bookmarks aren't really the primary way to keep track of things. As soon as you fly into/over things they will be permanently known to you and you can find them back through your galaxy map at any time regardless of bookmarks. When you're in the zone-information (or planet-information panel as I should call it) and you click on a bright icon for a known site-type it will automatically select the nearest one that you know. I desperately need to make another video to explain a few things.
Looking at your second suggestion some more, I might look into adding an option like "toggle marker" on all bookmarks and/or site-information panels but I would have to think about this because what's shown on the mini-map can impact performance etc. and there might be some counter-intuitive situations or complications with other things (not technical) that make it a bad idea that are not obvious to me at the moment. (I've thought about all these things many a times over the past years and often things are simple for a reason (not so much technical) but I just don't remember what they were (I've documented some of my thoughts but not every decision I've made).
The color differences on the mini-map b.t.w. are just land v.s. water, nothing to do with density of buildings. There are items (scanners) that you can get that can find the nearest sites within a certain range etc.
Having said all that I do agree with you there are situations where you sort of want to see more than just one thing marked on the map. I will just have to think about it more thoroughly how to keep such an improvement simple and non-ambigious.
As I'm thinking about it: Maybe when you just click on a bookmark item it should show it's location on the minimap (as long as you have that boomark's panel open in the context-panel) the context-panel or even the hover could also say the distance to the bookmark which would go a long way in determining which is the best one to use (e.g. when picking between two clinics).
EDIT: As I'm thinking: Because most of this stuff should go through the galaxy-map maybe clicking on the planet name or mini-map should bring you straight to the planet-information panel (so you don't have to go: galaxy-map -> click star-> click info->click planet
Let me know what you think.