Hi Blanch, that is looking great!
About those problem areas, this is how I would do it (maybe not the best way, but I am terrible with Creases and the Bevel Modifier with Bevel Weight only works in some cases for me…):

Having edge loops on both sides of the selected loops gives full control on how sharp/rounded they look, without artefacts.
The round cylinder has 8 vertices, while the rectangular piece has 12, so you need a 4 to 2 junction on both sides.
I just did this small part and only on one side, but you get the idea.
Personally, I would not use a Bevel Modifier at all, probably and only work with holding edges, but that’s just preference.
Didn’t show it here in Object Mode, with Subsurf, but it looks just as good as the rest of your model!