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"Wouldn't you think ProSeries should account for this (it doesn't)?"
Isn't that what you described? That the program has a place for you to enter this info.
The IRS has great reference materials.
From the W2 General Instructions guidelines for Box 12 codes:
"Designated Roth contributions.
Under section 402A, a participant in a section 401(k) plan, under a 403(b) salary reduction agreement, or in a governmental 457(b) plan that includes a qualified Roth contribution program, may elect to make designated Roth contributions to the plan or program in lieu of elective deferrals. Designated Roth contributions are subject to federal income tax withholding and social security and Medicare taxes (and railroad retirement taxes, if applicable) and must be reported in boxes 1, 3, and 5. (Use box 14 if railroad retirement taxes apply.)Section 402A requires separate reporting of the yearly designated Roth contributions. Designated Roth contributions to 401(k) plans will be reported using code AA in box 12"
"Taxpayer has contributed $4,000 thru qualified 401k plan thru work." <== seems to be Roth
"Can he still contribute additional $7,000 thru 1040 return?" <==into which type of account?
Everything matters: post-tax or pre-tax, employer or personal, in various combinations, plus this person's income level and age.
Have you read any web articles:
https://www.thebalance.com/are-you-eligible-to-contribute-to-a-401-k-and-a-roth-ira-2894148
https://www.investopedia.com/ask/answers/102714/what-are-roth-401k-contribution-limits.asp
The IRS has tables for this and articles, too.
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