Use a single GPIO for Multiple Uses (TMS320F2803x MCU)
This is typically fine, and also done in practice.

As you have already figured out, and the fine documentation tells you, you need a way to make sure that any peripheral circuits you connect to the affected pins are not causing mayhem when they see their inputs toggling at random, and make sure that they don't drive the pins unless specifically told so.

You must also look at the drive strength. For example, you may have an MCU that can drive an LED at 10 mA directly from a GPIO. While the LED would not care about a test signal driving it, the JTAG adapter will likely not be able to drive the extra load that the LED demands.

Another issue is when you're standing in the field to debug something, and realize that you have connected an essential functionality to one of the debug pins, so they can't operate simultaneously. Try to have less important functions here.

In summary: It's ok, but don't use them for critical functionality or load them down.