Of course a workaround could be to start 3 Boinc instances at the same time, each for one project and there I could limit the threads and remove the app_config.xml. But I was hoping for an easier way.

These issues are at the server side. Many ignore your local preferences. Especially the 0 priority setting.

Save yourself headaches and time.
Setup a different work queue for each offending Project or even a queue for a particular hard to manage WU.
I use a BOINC VM and assign it a current WorkUnit. BOINC FAQs describe how to create multiple BOINC installs for separate data directories.
Either way is a method of virtualizing a queue at the WU or Project level..

I don't mind checking each individual BOINC based VM's BOINC MGR, since they're in the same house.
However many users manage any BOINC port, that advertises itself, from a single BOINCTasks install.
BOINCTasks can communicate with, and manage, all your BOINC VM's/data folders on the your local host and across your network.

I spend a lot of time collecting projects at WUProps.
We have a great amount of experience with any project's quirkiness and managing a wide array of WU's.