Your RMD can be used as a good rebalancing tool. Take your withdrawals from the fund(s) that you need to trim in order to meet your desired asset allocation.
Or, if your funds are allocated the way you want them you could have Vanguard take RMD from all funds in proportion to their size. This is perhaps what you meant when you said they would take from all funds equally. This would leave your portfolio balanced. That is what I did last year and had the money put into a taxable money market fund. I haven't decided what I will do this year.
It also may depend on what you plan to do with the withdrawal. If you plan to use the money for expenses putting it into a money market account or fund probably makes the most sense. If you plan to reinvest all or a portion of the withdrawal into a taxable account you may want to give more thought to the process.
Personally, I prefer to keep the withdrawal separate from rebalancing.