Good question. I suspect that when you call, Taylor will say "shims are available only to certified techs" because they don't want ham-fisted owners messing up the neck set, metal screw inserts, etc. They stopped shipping truss rod wrenches with each guitar a few years ago for that reason. Last I knew the cost of a neck reset was pretty minimal. Many people could use a set of summer (thinner) shims for damp weather, and a thicker set of winter shims for dry conditions. I know people that have both summer and winter saddles, for example.
There is probably no real reason that you could not remove and lightly sand *your* shims down to achieve what you want. Go slowly and carefully a few strokes at a time with 240 grit sandpaper or even finer. Worst case, you ruin those shims and have to pay for replacements with a neck reset by a certified tech. If you ever take your guitar to a tech for adjustment, be sure to tell them that your shims are no longer stock. Otherwise they will see 0.009" (for example) stamped on the shim and replace it with the next larger size, not realizing that you need the same shim - unmodified - to get back to the original set-up.