Investigate use of --system-site-packages in venv setup in evergreen.yml

We pass --system-site-packages to venv when creating our virtual python environment. I'm skeptical of this flag and whether it is a good idea to use it. With the v2 toolchain we had a lot of packages in the toolchain and it caused a lot of difficulty. For v3, most of them were removed. Is this perhaps a vestige of an earlier time that we can now do without? It appears it was introduced in SERVER-20106 and forward propagated from there.

AC:

• Update any packages if needed
• If there are any new issues we should file separate tickets to investigate