I don't mind chamfering the pads but only when I install them onto old rotors. If you do it with new discs it can upset the wear of the disc and cause it to lip prematurely. The reason for chamfering new pads is to prevent the lip on the old discs rubbing before the rest of the pad hits the disc which can cause squealing.
I'd probably measure the discs and machine them if possible.
And I'd only use genuine pads.
I put ATE discs and pads in the 300e once and they turned blue from normal use!! Worse than that they caused the grease in the bearings to melt and seep out thought the end caps. Luckily I caught it in time, regreased the bearings and threw out the ATE's in favour of genuine parts.

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Andrew
300e 294,000mi
380sel 185,998mi
380se 309,980mi