I can't speak for the experts, but if it was me I'd try to get as much of the paint off as possible, so I'm free to sand and polish the underlying metal as much as needed to make it nice and smooth. I have an old apron that will be repurposed for a homebrew build and will likely get that treatment.
That ball trough runway looks like it might be a little steep. I'd double check that - if the peak is too high, the ball will slam into the leading edge of the ball trough baffle and result in unnecessary wear.
https://pinside.com/pinball/forum/topic/tweaking-a-ball-trough-and-why-you-should