Yes, you are right, the reason these transaction belong on line 8a is because they have no adjustments.
As long as the numbers are on your Schedule D, you won't have any trouble with the IRS. Box D transactions are fully reported to the IRS by your broker. As long as your gross proceeds match the 1099-B there will not be any problems.
I am not certain why you are concerned about this if you already have a Form 8949 with all of your transactions that you need to mail in anyway.
You can force these changes if you want to override all of your entries in the Desktop version, but you will void your accuracy guarantee and will not be able to e-file if you do.
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