Regarding the Line 29 vs Line 28... initially it appears to be wrong because the instructions on Form 8829 say:
Ln 8. Enter the amount from Schedule C, line 29.... .... See instructions.
If you then go look at the instructions booklet for Form 8829, Ln 8:
If all the gross income from your trade or business is from the business use of your home, enter on line 8 the amount from Schedule(s) C, line 29....
If some of the income is from a place of business other than your home, you must first determine the part of your gross income (Schedule C, line 7, and gains from Form 8949, Schedule D, and Form 4797) from the business use of your home. In making this determination, consider the amount of time you spend at each location as well as other facts. After determining the part of your gross income from the business use of your home, subtract from that amount the total expenses shown on Schedule C, line 28....
So when a percentage of business is conducted outside of the home, it appears that you take the percentage of the gross income attributable to the time you spend in your home office (this is one way to allocate it), and you subtract your total expenses on line 28.
More can be read on the topic at Internal Rev Proc 2013-13
https://www.irs.gov/pub/irs-drop/rp-13-13.pdf
Under Section 4. Application, .08 limitations, it mentions:
(2) The amount of the deduction computed using the safe harbor method provided by this revenue procedure cannot exceed the gross income derived from the qualified business use of the home for the taxable year reduced by the business deductions described in section 4.05 of this revenue procedure (deductions unrelated to the qualified business use of a home). Any amount in excess of this gross income limitation is disallowed and may not be carried over and claimed as a deduction in any other taxable year.
