Hey I was wondering if this type of emulation will be acceptable if I would decide to speedrun the game off PS3 CFW 4.90 via emulation or it's need to be PSN version, if not can somebody provide me with acceptable duckstation settings?

not sure what the method is that you are asking for on ps3, the way to play on ps3 that is allowed would be by having a disc and playing it on ps3 - not sure if your method would make use of the same built in emulation by sony.

either way though, ps3 is slow and your best bet would be to run on duckstation. default settings should be fine iirc, you just have to enable display options to show your settings in the bottom right of the screen (settings > display > on-screen display > show settings overlay).