I'm not an electronics engineer, but is it safe to shift 3.3v to 5v if the underlying hardware wasn't designed for that? Is there a chance to put too much strain on the power source?
You've got to stay under the engineered current limits on the provided 3.3v, including how much current is reasonable on all the wiring to your boost converter, but chances are good that mouse transceiver uses much less than the typical usb bus powered maximum current of 500 mA, and even at 75% efficiency, that's about 1 amp at 3.3v, which doesn't need thick wires or traces, or a big power supply.
The transceiver probably does use more power than a fingerprint reader, especially if the reader is idle, but likely not enough to worry about.
All that really matters is how much power (watts, i.e. voltage * current) the device draws compared with how much power the laptop was designed to output. Shifting the voltage doesn't really affect anything other than losing some power to conversion inefficiencies.
The computer doesn't know that it has a 3.3v line externally boosted to 5v. It doesn't care about that at all.
It can care about how much power is being used, since the upstream 3.3v power supply -- whatever it may consist of -- is a finite thing.
But power is not the same as voltage. A device running from 5v does not necessarily use any more or less power than one that runs from 3.3v does. We don't have enough data to quantitatively know if power consumption is problematic or not for this particular instance, but I very strongly suspect that it is not an important concern here.
Finally, computers (and computer-like things) definitely do care about signal voltage. But USB signalling voltage is the same regardless of supply voltage, with USB 2 working between ~0v at the low end and at most 440mV at the high end, and tolerating up to 3.6v for compatibility with previous versions -- by specification. So that's not an issue.
Tl;dr, it's fine. And the author did a fantastic job of executing this hack very, very cleanly.
I think I myself would have taken the easy route and found a good place to run a bodge wire for 5v, and maybe even stripped the Logitech adapter out of its housing for some good old fashioned soldering fun, but everyone has their own proclivities.
The "strain" would depend on how many milliamps your 5V device draws. I don't know the current consumption of these logitech dongles, but it seems to be adequately low for this hack to work.
The transceiver probably does use more power than a fingerprint reader, especially if the reader is idle, but likely not enough to worry about.