Two things can get your measurement all wrong:
Where do you measure the voltage? If you measure it at the power supply side, it's quite possible that you have a voltage drop in the cable and the voltage is much lower on the RPi side.
How fast do you measure the voltage? I have a cheap multimeter with a refresh rate of 0.5 seconds. Anything faster than that simply cannot be seen. Another expensive multimeter I own has a data logger mode with a sample rate of 0.001 second (it comes with a USB stick), which is enough to monitor the supply voltage. A cheap oscilloscope in trigger mode can catch voltage drops in nanosecond range. If your DMM is close to the first option, it's perfectly feasible for the Pi to complain about undervoltage which you simply cannot see.
As for the voltage you use, the power management IC (MXL7704) has the input voltage range of 4.0V to 5.5V, so you can't kill that one with 5.41 V. I don't own a Pi 3 so I don't know which other ICs are there which are powered with 5V. Find them out, google the datasheet and check how much voltage they can withstand. Do the same for all the USB devices you want to plug in. Then you'll know the limit.
Note that running at 5.41V (with only 0.09V of safety margin) will kill the Pi sooner or later. There will be a voltage surge at your local power plant, or the motor in an HDD will fail and dump some extra voltage into USB, and you will instantly find yourself over the limit.