The bolt tightening sequence, described as a spiral sequence from the middle outwards, can be viewed here.
I would guess that an unskimmed head is 134mm, because that's the spec for X25XE and Y26SE, between the upper and lower planed surfaces. So if it's measurably less then it has been skimmed. If it was skimmed because it was warped then the material removed might be significant.
Excuse my ignorance, but would you then have to use shorter head bolts?
A cowboy might do that. I very much doubt you'd bottom out a standard new head bolt regardless of how much you skim (assuming less than 1mm). Much more likely to be the wrong bolts, or the wrong washers, or you haven't correctly cleaned out the bolt hole.
Skimming the head ALWAYS increases compression. ALWAYS. It also brings the valves into closer proximity with the top of the piston. I've no idea what the normal clearances are in our V6's, but IMV the skimming limits on heads are usually to do with maintaining compression ratios within acceptable limits.
If you've skimmed the head by more than the allowable limits then the two options are 1) find a new head, or 2) fit a thicker head gasket.
As for the torqueing sequence. It's only valid for NEW standard head bolts. I'd guess these are 8.8 grade steel? If you use a stronger steel bolt (10.9, 12.9 or ARP fancy stuff) then following the torque sequence WILL lead to tears.