If it is a DA the answer is no. The problem there is not the transmitter. If you switch patterns with the transmitter on you will draw arcs across the RF contactor contacts in the phasor and the ATUs, causing them to pit and eventually to fail. In a properly designed phasing system the phasor master nterlock closure should drive the failsafe interlocks on all transmitters. Another reason for connecting the interlocks is that, should a contactor freeze in mid-excursion, the transmitter will not come up, preventing possible damage to the phasing system or the transmitter.
In 30+ years of working with DAs I have often come into an old station with a DA problem and found that the problem was due to a phasing system that was not properly interlocked with the transmitter.
If you are talking about a non-D the answer is still no. The transmitters should be interlocked with a system that prevents them from being connected to the antenna system at the same time, which could damage one or both.
How long a "burp" you have to put up with when switching depends entirely upon how long it takes each transmitter to go from the RF off (or as I still tend to call it, "plate off") command to zero RF output.