Can't decide - install modules with Ubuntu package manager (apt) or pip3 in venv

[snippsat]

I may not even use any programs that cause conflict and I'd just be overcomplicating things with venv for nothing.

Yes you should just try,pip can also uninstall.
Virtual environment is build into Python newer version,so it easy to try that first.
It work for me if i do a quick test,don't find GPU as i now run Virtual-box.

# Make environment 
tom@tom-VirtualBox:~/Documents$ python -m venv watt_env

# Cd in
tom@tom-VirtualBox:~/Documents$ cd watt_env/

# Activate 
tom@tom-VirtualBox:~/Documents/watt_env$ source bin/activate

# Test pip,it point to this folder as it should
(watt_env) tom@tom-VirtualBox:~/Documents/watt_env$ pip -V
pip 19.0.3 from /home/tom/Documents/watt_env/lib/python3.7/site-packages/pip (python 3.7)

# Clone Repo
(watt_env) tom@tom-VirtualBox:~/Documents/watt_env$ git clone https://github.com/BoukeHaarsma23/WattmanGTK.git
Cloning into 'WattmanGTK'...
remote: Enumerating objects: 6, done.
remote: Counting objects: 100% (6/6), done.
remote: Compressing objects: 100% (6/6), done.
remote: Total 753 (delta 0), reused 1 (delta 0), pack-reused 747
Receiving objects: 100% (753/753), 578.10 KiB | 1.14 MiB/s, done.
Resolving deltas: 100% (487/487), done.
(watt_env) tom@tom-VirtualBox:~/Documents/watt_env$ cd WattmanGTK/
(watt_env) tom@tom-VirtualBox:~/Documents/watt_env/WattmanGTK$ ls
LICENSE  README.md  run.py  setup.py  WattmanGTK

# Test Python
(watt_env) tom@tom-VirtualBox:~/Documents/watt_env/WattmanGTK$ python -V
Python 3.7.3

# Run install
(watt_env) tom@tom-VirtualBox:~/Documents/watt_env/WattmanGTK$ python setup.py install
running install ....

A couple of error,need to install this.

sudo apt-get install libcairo2-dev
sudo apt install libgirepository1.0-de

Run install again.

(watt_env) tom@tom-VirtualBox:~/Documents/watt_env/WattmanGTK$ python setup.py install
.....
Using /home/tom/Documents/watt_env/lib/python3.7/site-packages
Finished processing dependencies for WattmanGTK==0.0.1

Installing different versions in root (sudo apt) and in a non-root directory (pip -user) both provide global access and does not avoid conflicts. Is this correct?

If using pyenv Simple Python Version Management you safer from start,as it never mess with system install of Python.
It dos install Python version wanted(eg 3.7) and make it a system wide installation.
If all goes wrong just go back to local system pyenv local system.