Is there anything other than "Game Level" that can be changed? For example, if the power-up method is "SemiAuto", I'm forced to equip the laser after equipping two options. (Gradius IV has poor lasers except for Type-F). The default Hit Size is "Small", which means the hit detection is smaller than the original version. Wait Level is not available in the PS2 version, and lags when set to the default setting of "1" in the PSP version. Also, if you set the screen size to the default "Full", the screen is stretched horizontally, which is uncomfortable.

As long as Game Level meets the category and Extend/Life keeps the default setting: I don't see an issue changing the others for the benefit of the speedrun.