Power on configuration for MCU using CPLD and pin multiplexing
It looks fine to me. It fits with the description you gave. I think this is basically what the MCU vendor had in mind.

Only additional thing you should consider, is what are the "Other components" do during the boot period. More specifically, how do they influence the CONF1/CONF2 signals. It could be that they also pull the lines to one direction (not actively of course, but due to internal pull-up/down or through the ESD diodes).

If it is the direction that suits you (the same as the CPLD) then all is ok. If not, there could be problems, depending on which side pulls stronger. If this is the case, you could/should use "isolating" components between the "Other components" and your MCU/CPLD structure.

That is most commonly series resistors that limit the current and thus the influence that the "Other components" can have to the configuration signals during boot.

OFF-TOPIC: I'm just asking myself why do they recommend to use a CPLD for something that simple?! Why can't you just use fixed pull-up or pull-down resistors?