You mean an object that has alpha in its texture or material? Can you show a screenshot?
Regarding retopology in general, though, there is a design task for implementing a better retopo workflow in Blender, including a new shader to deal with visibility issues related to backfaces and the retopo mesh + base mesh:
https://developer.blender.org/D5919
This will probably take a while to complete, though. It’s not their #1 priority.
In the meantime there are a number of great addons for retopo:
PolyQuilt by Sakana3 (highly recommend reading or at least skimming through that thread)
RetopoFlow by CG Cookie (not sure what the status of 3.0 is)
SpeedRetopo by Pitiwazou (forum thread here)
Poly Source might also be useful
I’m pretty sure I saw another good one on github somewhere but I can’t find it at the moment.
I HIGHLY recommend getting Cirno’s latest Box Select X-Ray addon so you can box select without being forced into x-ray or wireframe. It has a lot of custom options.
There’s a design task for getting some sort of select-through in Blender but it is not going anywhere fast even though it is a frequently, requested, feature.
Which keymap are you using? In the Industry Compatible keymap 1/2/3 in the 3d viewport switches directly to that mode. If you’re using one of the other keymaps you can edit your map to make it work the same way. (3D View > Object Non-modal; not sure if you need to change more than these 3 or not; the keymap editor is a mess)
It’s kind of a ‘known thing’ that the UV editor needs a lot of work to be up to snuff but there’s no design task for it. Hopefully that will come after 2.83.
I haven’t tried UV mapping in Blender yet but there’s an addon that ships with Blender but is disabled by default called UV Magic that has some extra tools.
There is also a forked version of TexTools for Blender 2.8x:
I think this is the download: https://github.com/SavMartin/TexTools-Blender/releases
And here’s a discussion thread: TexTools for Blender
I hear it has a few issues (see the most recent posts in the discussion thread) but I think most of it works.
There are also some UV packing addons like UVShotMaster and UV Packmaster but I’m not sure if those are for your particular workflow.
Benjamin Sauder had a useful-looking UV tool for 2.79:
Branch for 2.8 compatibility seems abandoned, though: