These notes are present to just provide information to the developer regarding some features present in PSoC Creator or any violations that occur in the design. They are harmless to the project itself and I don't think can be removed in any way.
The notes you provided are the most common ones that we see, which tells us that the pins P6 and P6 when used as SWD/JTAG pins, the usage of additional functionalties present on the pin like uart, spi etc. will be prevented.
In the Systems tab of the DWR window, if the Debug select is chosen as GPIO, these pins can also be used to make use of the other functionalities.
Please refer to this KBA to get rid of error or warning messages: GCC Warnings Diagnostic in PSoC Creator - KBA225431
Thank you for your reply! I will ignore these messages!