There are two Preferences:

Project > Preferences
Computing > Preferences

I am using Project > Preferences and it seems to work.

Should Computing > Preferences use the same set of Preferences as Project > Preferences?

Or maybe there will be multiple projects in the future?

Both preference pages work but do different things. Project Preferences (on the website under Your Account > Preferences) lets you choose which Axiom apps to run — you can select CPU only, GPU only, or both. Computing Preferences (in your local BOINC Manager) controls global machine settings like CPU usage, disk limits, and when to run. They are independent — the website tells Axiom what type of work to send you, the local settings tell your machine how to run it.

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Thank you for the explanation!

I use local preferences set in the BOINC manager Options > Computing Preferences because I run multiple BOINC projects. FWIW: I have found web-based local preferences buggy when using multiple BOINC projects.