Hi senhaku, this is a question for koji

Personally I don't think there will be any noticeable impact on the pc performance. (Only exception would be if yu 'll be using any ancient machine that'll meet XP minimal requirements (it was 128MB RAM, 300Mhz i think). Most of the time winflip is waiting in background eating minimal resources (about 600kb of Ram), it uses some CPU and about a few megabytes of RAM only when you enter flip mode.
Capture image when a new window appears -> it was added in Winflip v 0.5, in previous versions winflip captured windows textures every time you opened a window. This mode had some compatibility issues with some applications (Outlook bug). So in 0.5 WinFlip refresh window textures only when you enter flip mode. (That's how koji explained it to me

Use system meory instead of video memory -> It seems to me as a compatibility option either for older graphic cards, or maybe for a mobile graphic chips like Intel GMA. I don't use it mnyself, but I guess it just does what it says resulting in a larger RAM consumption.
Hope it was helpful ^^b