A SEP contribution can be made at any time of year which makes Vanguard's statement that they permit a SEP contribution until the end of the year meaningless. However, any SEP contribution made after the due date of the tax return for the previous year (including extensions) can only be a SEP contribution for the current year. As I said, Vanguard is not the one who "applies" the SEP contribution to a particular year. Vanguard only reports on Form 5498 the amount of SEP contributions made in a particular year, not for a particular year. It's your responsibility to track and report the contribution as being for a particular year.
The SEP contribution that you made after October 15, 2019 can only be a contribution for 2019, therefore it is a SEP contribution for 2019 and it must be reported on your 2019 tax return (unless you obtain a return of contribution). If you will have sufficient income from self-employment in 2019 to support the amount of this SEP contribution for 2019 already made, nothing else needs to be done with regard to this contribution. If your net earnings from self-employment in 2019 are sufficient to support more than the amount of SEP contribution already made for 2019 you have until the due date of your 2019 tax return, including extensions, to contribute the additional permissible amount if you so choose. If your net earnings from self-employment in 2019 end up being insufficient to support the amount of SEP contribution that you've already made for 2019, you have an excess contribution to deal with.
I have no idea what you are referring to as an "employee IRA" or how that contribution has anything to do with your SEP contribution. If you mean your SEP IRA, how is it that you already know the maximum that you will be eligible to contribute? The year is not yet over and you likely are not yet able to determine your net earnings from self-employment.
The law does not permit the extension of the SEP contribution deadline beyond the due date of the tax return for the year for which the contribution is being made (October 15, 2019 in this case, assuming that you filed a request for extension by April 15, 2019). The IRS has no authority to waive that deadline.
