You may as well just throw a fiver in the bin every time you buy a bike as that is effectively what you will be doing.
If they supply pedals you will be paying for them in the price. They are probably not going to be pedals you want so they are going straight in the parts box/jumble/charity pile.
Admittedly if they put something decent on there might be a small increase in the possibility they will be okay for you and certainly they will have some value to sell on if not but there doesnt seem to be any point.
If they supply flats or SPDs then which flats? Which type of SPD? Do they list bikes with flats and SPDs separately (same model) or just choose which will have which?
Personally I would rather manufacturers stopped supplying rubbish OEM stuff that come straight off a bike and reduced the price a little bit – in particular tyres. I think tyres and pedals are the two parts you are most likely to take straight off a bike. Grips you can generally live with and it’s only really those who need large grips that have a problem but they are the minority.
Grips and saddles will still function as a grip and saddle regardless of whether the person actually likes them but pedals might be completely unusable to some people. I don’t own any flat pedal cycling shoes so a bike with flats is un-ridable to me, likewise a lot of people dont have SPD compatible shoes.