The taxation of a return of contribution is described in CFR 1.408A-6 Q&A-1 (<a rel="nofollow" target="_blank" href="
https://www.law.cornell.edu/cfr/text/26/1.408A-6">https://www.law.cornell.edu/cfr/text/26/1.408A-6</...>). A return of contribution is a distribution from the Roth IRA. The amount of the contribution returned is a nontaxable distribution of basis, but the gains are taxable on the tax return for the year in which the contribution was made. As a distribution from the Roth IRA, the gains are taxable in the manner that any taxable distribution from a Roth IRA is taxable. All taxable distributions are subject to an early-distribution penalty unless you have an exception that applies. Being the gains on a return of contribution is not an exception in the tax code.
I doubt that this was intended to be punitive, it's just a consequence of the way bits and pieces were added to the tax code over the years, perhaps an intended consequence that the lawmakers chose not to change.
Yes, if the gains are substantial, there are circumstances where it can be beneficial to pay the 6% excess contribution penalty one year then resolve the excess the next. I've done this myself. Correcting an excess contribution after the due date of your tax return and after having paid the 6% penalty for at least one year does not require the attributable earnings to be distributed. The excess can be resolved by either applying it as part of a subsequent year's Roth IRA contribution or by making a regular distribution. The regular distribution will not be taxable because it is a distribution of contribution basis (even though that basis may have come from an excess contribution).
