How can I selectively copy preferences from one machine to another?

There is no rigid standard on macOS for location of preference files, nor of data. This is particularly true for apps from outside the App Store.

• Is it sufficient to copy the preferences files from ~/Library/Preferences?

Only if the app keeps its preferences in ~/Library/Preferences.

Some apps will have preferences inside: ~/Library/Containers', or '~/Library/Application Support

• Will there be any side effects to doing that?

There could be. For example, a preference which points to a physical location in the file system.

The app may also keep data in other locations within ~/Library. If you are lucky in ~/Library/Application Support, but could be elsewhere. Further, if an app has computer wide (not just user) data, it may keep preferences and files (e.g. licenses) in /Library or somewhere in /Users.

Licenses can be particularly tricky as they are often partially hidden.

• Will I need to ensure that apps are closed when I copy the file?

Safer to make sure that the app is closed. Probably not essential.

• Will I need to reboot to flush anything from memory?

In most cases no, but it could a wise precaution.

Further thoughts

I hope I have convinced you that there is no guaranteed way of transferring the required data from one computer to another. Even Migration Assistant is not 100% - it is only an assistant.

Though a few apps will be easy to transfer, you will need to check each one as you go.

But I do favour the "fresh start" approach to a new computer. Make sure you have all your license information before you start.