I admit up-front that this question may be the result of unfounded paranoia. But I am concerned that uploading and downloading data in binary form opens the door to exploits that might not be possible if the data were encoded during transfer and decoded at the destination.
I will stipulate definitions because I see the term "binary" thrown around a lot and I am not sure if everyone means the same thing when using it. When I say "binary" in the context of this question, I mean a stream of bytes that may have the high order bits set in at least some of those bytes. I don't mean a stream of bytes merely representing binary data, such as base64 encoding.
I am imagining that in the lowest levels of some possible network protocol used for Internet data transfers, there might be various "handshakes" using bytes with high-order bits set. If this were true, then a web server or browser that accepted arbitrary 8 bit streams of data could become vulnerable to some forms of attacks that employ some kind of "handshake doping" or the like.
I might agree that at the web server/web browser "level" of the data transmission hierarchy, perhaps this issue is irrelevant. That is what I want to know: Is a web "connection" (handshake and associated data transfers) immune from manipulation this way?
I'm not asking for advice on safeguards and recovery; I am only asking if there is a possibility of the kind of scenario I am suggesting.