There are many ways to answer this question but ill just choose one ( notice im stalling while i think of something profound) ...

Like 1:1 scale cars, if they blue printed them, got them to put out max horse power, with nice exhaust and tranny and diff to support it, a daihatsu charade would end up costing some $40,000.00 to buy as opposed to $13,990.00 drive away no more to pay..( got that from an ad) Same as the cost to develope an engine is incorporated into the cost of its final unit price.. to keep costs down RnD is kept down. Also to make a motor that has conservative port timing will allow the manufacturer to use less expensive raw materials to increase their botom line,, Ive only ever mapped one engine that you couldnt mod ! the rest have something or other to cut out or modify ,
I recently did a 21 V Spec, the owner wanted less aggressive bottom end , linear powerband with extended tops.. Now thats what he needs from his motor, this guy is a good driver and competes in buggys regularly and has decided what will give him the edge.. so i gave him what he wanted by altering the charachteristics of the engine.. hes as happy as a pig in mud ! so Modifying isnt just about getting it to go as fast as possible .. its about getting it to respond the way you want it to (and go as fast as possible)

Also to machine an engine the way you need to in order to get it to perform costs money and time, you would be supprised how many manufacturers cut corners by only doing one pass cutting as opposed to 2 or 3 to do the job correctly, i mean it may only cost them 12 cents to do the extra but time that by 1000 engines a day etc etc you get my drift ... hey there goes that drifting thing again... lol

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So ... um yeah thats why we modify engines

Hope this helps
MM