You shouldn't have an amount in Box 4. If there was federal tax withheld, it should have been reported in Box 2. There should be no entries in Boxes 3-6 on your W2. If there is an entry on Box 4, you would need a corrected W2 to show federal tax withheld.
Yes, if there's a correct amount reported in Box 2 instead of Box 4, then federal income tax was taken out of your pay. You still owe self-employment taxes, and that is the option to choose to pay your taxes.
The biggest concern is this. If your W2 has an amount in Box 2, it's ok. If has an amount in Box 4, just as you mentioned, then you need a corrected W2 to show that federal income taxes were taken out, and these need to reported in Box 2.
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