No, there is no difference in the ability to increase your basis for major renovations if you write your check to an individual or a company. The expense "counts" either way.
It isn't common for the IRS to ask for "proof" but it is always wise, of course, to keep the documentation. Your contracts and receipts serve as that proof, no matter how you write the check (or even if you pay with cash and have no check at all).
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