Yes, in most cases, how the income is reported can make a difference on your tax return.
Form 1099-MISC Box 1 reports "Rent," which is reported on Schedule E and not generally subject to self-employment taxes.
Box 7 reports "Non-Employee Compensation," which the IRS interprets as Self-Employment income for Schedule C. This income is subject to SE Tax.
If, however, you report your rental activity as a business (Schedule C), then both Box 1 and Box 7 would be included on Schedule C and subject to SE Tax. In this case, how the income was reported would not make a difference on your return.