Sorry for the delay in getting a response back. Both of these issues seem like bugs to me. The good news is they are both easy to replicate, so I will send bug reports to the developers. Also, as far as I can tell, they are just visual bugs and are not affecting the model logic at all.
Lopsided Legs:
For the first issue with the lopsided legs, it seems to be related to the Height Rule of the legs, and/or an issue with connecting to another downstream conveyor that is facing the same direction and is a similar width.
For the Height Rule (in the Conveyor Visualization Properties) if you use the first option, "Leg Height Following Conveyor Height", the legs will look fine in the model, apart from not touching the ground all the way through the slope. It's the other two options that cause the legs to be lopsided. So you could create a separate Visualization for just these problematic conveyors and use the first Height Rule option.
When a sloping conveyor (either sloped up or down) is connected to another conveyor that is the same width and going the same direction, FlexSim tries to adjust the legs to match a little better. So in your model, if you were to disconnect conveyors “IPF1_9B”, “ISF3_1B” and “IPF2_6A” from the next downstream conveyor, the issue goes away. As a workaround, you could connect the two sections of conveyor with an A connection instead, but the new visuals may not look how you want either.
Interestingly enough, the amount of slope there is on the sloped conveyor affects the length of the erroneous leg. One side will look fine, but the other side will look longer or shorter (depending on if the slope is up or down).
Side skirt and legs:
As you've seen, the size of a side skirt affects the size of the legs. So when the size of a skirt is large enough and the conveyors are close enough to the ground, the legs can poke through the conveyor. Even adjusting the leg height and height rule doesn't seem to make a difference - at least in a way that makes it look better.
The draw code of the conveyor system isn't really accessible, so I don't know how exactly the skirt and legs work together. I also haven't found anything else to adjust the size of the legs independent of the skirt. Unfortunately, that means the only workaround I am aware of is the one you already mentioned in the question - make sure the skirt is small enough so the legs don't poke through.
