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The 501c3 tax status is convenient for receiving certain grants and other large donations. I think that you misinterpret the concept of being "under the authority of the Federal Government". First most all Churches are NPO's (non profit organizations) and thus are corporations. Nothing wrong here as it is the means by which a Church can (among other things) have its own bank account, pay its own employees (a salary for the priest is nice), take out insurance on its building, property and liability, and maintain its tax exempt status. As a non-profit corporation a Church can also receive donations which can be claimed as charitable contributions by the doner on their own income tax, a Church can also be exempt from property and income taxes so that the government isn't taking a portion of its income. A Church that is not a corporation cannot do any of these things - it has no legal standing at all.

The 501c3 is tax category of the IRS (federal taxes) and most granting bodies (whether governmental or not) require that the recipients of grants have some kind of 501c3 authorization. This insures for the grantor that they are indeed giving money to an organization that can monitor how that money is used and provide some accountability that it was actually used for the purpose for which it was given.

If a non-profit corporation applies for 501c3 status, it agrees to abide by certain regulations that are set out by the IRS for accountability and reporting purposes. That's all the "governmental authority" that is exerted. Beyond the reporting of income and how it was used, there is no other control by the IRS that is exerted.

Many Churches find that the 501c3 status is beneficial to their ability to raise money and accept donations at relatively little cost to themselves (I think the filing fee for the 501c3 is $100) and increases their ability to do charitable work far beyond their individual ability. But to answer your question - not every parish is a 501c3.

Fr David