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It seems the IRS would have more money from the person (from SE tax).

The IRS doesn't really 'have' money. They are a pass-through that collects money and sends it on to the appropriate place - in this case the SSA. If the SSA is operating at break-even or a deficit, it will be sent back out to recipients. If the SSA has more revenue than needed, the money will go into the 'trust fund'.

What risks would there be of owing the IRS a big amount later on because of additional taxes or penalties?

None for the individual taxpayer, as long as they paid the SE tax for the year they got the 1099. For the employer - some big risks up to and including pretty significant fines, and possible imprisonment for improper withholding and non-payment of required taxes. Additionally, there actually have been cases where workers initially classified as contractors were awarded back wages when it was determined by the DOL that they should be employees:
https://www.dol.gov/whd/media/press/whdpressVB3.asp?pressdoc...
http://www.nola.com/business/index.ssf/2014/03/metairie_jani...
https://www.dol.gov/newsroom/releases/whd/whd20140827

AJ
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