luckily enough the 4age is engineered in way that makes it easy to figure out changes...... ive been playing around for the same reasons as you. at any rate with standard bore on the block you can figure roughly for every MM you lose in material of the head/block mating surface to gain approximately 1 full point of compression. so your figuring is correct. you should have 9.9:1 compression. with 0.5mm overbore it will be a little less than a full point, i dont have the formula's in front of me but they are out there.
to my knowledge the stock bigport pistons are 9.4:1 not 8.9, the 8.9 were in later spec, MAP based GZE's
its hard to say how much a machine shop will take off the mating surfaces, generally they will take as little as possible to make it flat, which of course varies. if you tell them you want a specific amount shaved they will do that.
personally i would only have them remove the minimum amount and then use the proper head gasket thickness and pistons to achieve my desired compression ratio
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