Temperature settings not changing in Cura
You're right in that the profile overrides the material. Cura's overriding precedence is as follows, where higher numbers override the lower numbers:


Cura's base defaults.
Printer specific settings.
Adjustments to the printer made in the Machine Settings dialogue.
Nozzle profiles.
Material profiles.
Quality levels (aka built-in profiles).
Custom profiles.
Settings not yet saved to a profile.


In the Cura GUI, once a setting has been saved to a profile, there is no way to really get it out again. You can only create a new profile and copy over all of your overrides.

However for the temperature you can still click on the little fx button next to the setting. This will restore the link from the setting to inherit again from different settings. In the case of printing temperature, the material profile actually adjusts the "Default Printing Temperature" setting. Clicking the fx button makes it go back to "use the Default Printing Temperature" so that your material's temperature is used again.

The same does not go for fan speed, sadly.

The Cura developers are planning to remove the fx button and replace it with a button to remove a setting override from a custom profile. That would fix your problem. It's not implemented yet though.

Source: Am Cura developer.