The pass through deduction just phases out for physicians (and many other occupations). We're absolutely eligible for it.
The $329k limit takes into account business deductions, pre-tax retirement contributions, self-employed health insurance premiums. So it's either looking at your AGI or something close to it--I can't remember exactly. I'm sure the link above specifies it.
There are many ways to get your AGI down to be eligible for the deduction. Most independent contractors making under $450k I would think could take full-advantage of it. Above that you might need to start looking into some pre-tax pension plans and other creative stuff.
If I'm in the situation one year where my deductions bring my AGI under that $329k limit, then I'll often switch from making pre-tax 401k contributions to post-tax Roth 401k contributions so I can maximize the pass-through deduction. (Under $329k, your deductions and pre-tax contributions become less valuable because they decrease your pass through deduction). WhiteCoatInvestor has an article on how to optimize that deduction, going over both the pros/cons.
If you have other sources of income (real estate, W2, etc.) then things get a lot more complicated I think. Fortunately all my income is 1099 income, all from being a physician, so it's straightforward for me.