I feel sorry for you... because you are exposing your misunderstanding of how flash actually works.
Here I faced with a serious dillema: usually the way I select a tool to use time-to-time is by trying how it works. Since I'm severily limted to one (and only ONE) - yes ONLY one - ISO, I need to somehow pick it out of many - without testing, right? Or, do you suggest me to copy fist one thousand of files to my dear Flash, run it once, then wait 20 min until they are all erased (because I don't like that one), then copy another one thousand files to my (now pure) Flash.... and go on, until the very last ISO in your carefully pre-tested list is done, and I finally happy with it - right?
It usually doesn't matter if you copy a single large file or multiple small ones, since (nearly) the same amount of sectors will be used. In fact, if you format your flash using a 2k cluster size, exactly the same amount of sectors will be used (because ISO9660 uses at least one 2048 bytes sector per file). The wear and tear comes from the sectors used, not the number of files. Ergo, it doesn't matter if you copy ten thousand small files or one ISO that contains ten thousand files, the end result with regards to wear and tear is exactly the same.
Oh, and if you want to displace the debate to the fact that it usually takes more time to copy many small files than a large ISO, and that deletion takes time, remember that I already acknowledged copy time as one of the few advantages I saw in using a method that deals with whole ISO, and remember that when dealing with ISOs, Rufus currently starts by formatting the whole drive, which is very quick (unless you're foolish enough to uncheck quick format) and means you don't have to delete a thing.
What you are trying to perform here has a name: FUD.
Yes, EXACTLY as it would if you used G4D and copied whole ISOs.
So, lets calculate: 5 thousand files droped on the Flash during 3 days being a regular Joe - my Flash is no more, its actually gone
Another Addon: Modern flash media also have circuitry that prevents wear and tear even if you are rewriting the same flash sector over and over => this mean that even in the case of a file system that is using the same sector as directory index, or if we somehow were to write the MBR 10000 times in a row, different physical locations of the flash are actually written each time.
By all means, please keep trying to discredit Rufus, because this is becoming highly entertaining...