I think the retirement deductions will work the way that other similar deductions work: SE health insurance, SE taxes, etc. Let me give you an example to illustrate and then provide a handful of reasons explaining why I think what I think.
EXAMPLE:
Suppose someone married earns $100K as a sole proprietor, has a spouse that earns $24K in W-2 wages, and deducts $10K for SE health insurance and another $10K for SE taxes and then takes the standard $24K deduction.
This taxpayer's taxable income equals $80K ($100K+$24K-$24K-$10K-$10K) and this taxpayer's qualified business income (QBI) equals $100K...
But what the Sec. 199A deduction equals is lessor of 20% of the $80K or 20% of the $100K... so $16K.
Now if the taxpayer also does a $20K pension, I think that just plugs in like SE health insurance and SE taxes. I.e., it doesn't impact the QBI. But the $20K of pension drops the taxable income to $60K, so now the Sec. 199A deduction equals $12K.
In summary, pensions don't matter to a sole proprietor's or partner's QBI but because they reduce taxable income, they impact the ultimate Sec. 199A deduction.
WHY I THINK THIS:
To know for sure how these items will be treated, I think we want to see what guidance IRS provides next month. But five reasons stand behind my reasoning:
1. The taxable income limitation already "accounts" for the pension stuff for many folks.
2. For S corporations, the pension deductions (and also SE taxes and SE health insurance BTW) do get deducted from QBI given the form where they appear. So what you're really talking about are some sole proprietorships and partnerships.
3. Congress in the statute did specifically indicate that certain items were not part of QBI... for example, S corp shareholder wages, partner guaranteed payments, etc. If they had wanted to exclude pensions, SE health insurance, SE taxes from QBI of sole proprietors and partners, they could have done that.
4. Making the deductions dependent on each other would be complicated. And Congress and IRS opt for simplicity in the accounting in other situations. E.g., SE taxes get applied to 92.35% of SE income. That basically lets self-employed person not pay SE taxes on the employer half of SE taxes but without having to make a circular calculation.
5. In my "Maximizing Sec. 199A Deductions" monograph, which thousands of CPAs and attorneys have read over the last few months, no reader has disagreed with my description above. BTW, some readers have disagreed with my description of whether or not Sec. 199A applies to real estate investors. This isn't a super weighty factor... but it suggests many other accountants learning the new law agree with me.