However, there are more "traps", for example 1) if the application is such that there is no guarantee for no character arriving at Rx during reset, the bootloader might get activated errorneously. Also, 2) certain applications might not tolerate the delay in starting the user code.

while these are valid concerns I want to add
1) is rare and if you have that problem insert an AND gate between the transceiver and the uC anding the serial data with something the user code activates and make it possible with a switch or whatever to disable the "user code condition".
2) I have never seen that one except where stupid hardware mistakes (e.g. driving something active when a port pin is high) were covered up by software.

Erik