If you're rolling over a roth from somewhere else, you may have more than the 5,500 contribution amount. Therefore you can obviously go into more than one fund.
However, if you don't, and this is your first time investing in an IRA, then obviously that is a bit harder. However, I think you're misunderstanding a fine line. An IRA is just a holding tank for funds. You can have the same exact funds in an IRA as you could in a taxed account. It's just that you're earmarking the holdings as "for retirement" for tax purposes.
So what does this mean? Well it means that Vanguard isn't actually requiring a 3,000 minimum on funds in your IRA. Instead, that's just what the fund is requiring. So therefore, you just have to find funds that don't have the 3,000 minimum.
Take for instance the S&P 500 index fund. It's available in a regular mutual fund "casing" (for lack of a better word) which does in fact have a 3,000 minimum, referred to as investor shares (VFINX). However, it's also available in an ETF "casing" (VOO), which does not have a minimum. So you could invest into it as an ETF until you reach the 3,000 mark, and bump it up to the investor shares, which will then bump you up automatically to the admiral shares version when you get above 10,000. Not all funds have a lower/no minimum version, so you may be limited at first, but that will get you started.
At least that's how I understand it. Other mustachians, if this is not the case, please correct me.