VirtualEnv copies PIP and SetupTools, in case you want to install new packages in the virtual environment (which is the main reason for VirtualEnv's existence).
So, the only way that I see (if you don't want them), is to create the new virtual environment from command line, and then "import" it in PyCharm.
Regarding the 2nd dilemma, it (might not be your case, but) sounds like an PyCharm caching problem. In [JetBrains.IntelliJ-Support]: Package requirements not satisfied (though they are), Sergey Karpov states:
Please try to remove this interpreter from IDE, then do File | Invalidate Caches/Restart.. | Invalidate and Restart and add the interpreter again.
Edit #0
I made a confusion: I talked about VirtualEnv, when in fact it's [Python 3.Docs]: venv - Creation of virtual environment that' being used. Nevertheless, this doesn't change much, the problem still persists, but only the --without-pip options is present.
Regarding the other problem, as I specified in a comment, I tried reproducing the behavior on my laptop, but I couldn't.