No, it's no harm, and it doesn't necessarily mean lower quality media either - you could have horrible media and it could just as easily have a very fast lead-in time. Having said that, if the drive in your Mac is proprietary and would be a b!tch to replace, you may want to use your cheaper, easier to replace drives for the bulk of your burns (they are likely better drives as well).
BTW, 'flashing' and 'crossflashing' are two slightly different things. Flashing would be to simply update the firmware. Crossflashing would be to update the firmware with one specially made to 'change' the drive to a different one. Your Plextor is simply a Benq 1640 using Plextor's firmware instead of Benqs, but using Benq firmware will perform better, for one thing you'll be able to use QSuite (Solidburn, etc.) with it. The OEM, in this case Benq, usually updates the firmware more quickly and often than the rebadged brand, in this case Plextor. It's not to say that the Plextor firmware is junk, but flashing it to a Benq will put you further ahead of the curve in terms of firmware, and firmware is a key to burn quality and the overall performance of the drive.