@nativecoruscant
Ok, downloaded the lot and took a look at all 3 issues you've posted about. Once I saw that you were remodeling someone else's lot, I also hunted that down and downloaded that one too to take a look at it to get an idea of what changes you're making and to see if the issues you have were there on the original lot. From what I could tell after looking at both, is that you are adding basement levels for what appears to be underground garages and entrance tunnels to get to them mostly.
In a nutshell, I think two of the three issues you have are caused by how basements work coupled with the use of platforms which have their own unique issues. Basements and platforms simply don't work together very well to begin with, and basements are set up to not be seen when looking down from above ground for the most part and above ground doesn't show when in the basement looking up (without changing a few game files - not a good idea imo). That's not something we can do anything about, it's just the way the game works. But I have tried to come up with some things you can try to mitigate the worse of it. So, on your issues in order.
1 - The lines are the rock floor tile bleeding down from above for both the garage door and at the pool. And I'm pretty sure platforms are the cause. At the pool, as best as I could tell, it looks like the entire 1st basement level is a platform over the actual floor so it could be the lower platform or a combination of the two platforms not getting along as both change the normal wall height. At the pool, you could change it to terrain paint, and it goes away, although, there is not a terrain paint in the game that is that dark or has that rock appearance. You could try blending several terrain paints and maybe get a better shade. If you do decide to go that way, that probably means replacing all of those tiles throughout the build with it just to keep the aesthetic and things match. A lot of work for little gain really. Personally, I'd delete the tiles under the plants, add a couple more along the side wall until all the bleed over is gone and use the darkest dirt terrain for that area. But at the garage door, that won't work. But it might not have to be changed anyway. When I installed the lot, that issue did not show up at all there. It was fine all six times I installed the lot during testing.
2- I think this is happening because the entire floor on that level appears to be on a platform but am not sure about that. I did find that narrowing the pool by one tile fixed it though.
3 - What is going on at the bridge is sort of a combination of things. The same thing is happening further down near the end of the entrance tunnel to. It's nothing new really as I have seen it happen on second story porches, balconies, etc. with fences. Above ground, I usually add an exterior wall trim on the edge, but I found during testing that that doesn't work in a basement. After I closed my game, I did think of something else you can try though. See if you can delete the ceiling below that bridge and change the lights to wall mounted. I don't know if that will work but I do know that what you are seeing is the ceiling below because the floor itself is invisible from the side.
And another issue I ran into with the lot FYI. When I tried to install the lot, it locked my game up twice completely where I had to force quit before I got it to install the first time. It locked up when installing from the map and when I didn't bulldoze the lot that was already there. It finally installed after bulldozing. So, you might want to consider noting that in the lot comments if you are going to post the finished lot to the gallery. Folks need to bulldoze before installing.
Hope this helps.