I bought only the pdf of issue 1, and while the multiple files gave me a bit of a pause at first, I'm definitely in favor of keeping the files broken up like this. Loading/scrolling time isn't much of an issue, even an work, but like others, being able to make multiple directories once there are more issues will be a major benefit for me.
I'm also in favor of being able to choose whether to download the single file version, the multiple file version, or both.