Regarding #2, section 415(c)(1)(B) limits one to contributing 100% of the participants compensation. In this context, compensation is reduced by the amount of the employer contribution, but not by elective deferrals or Roth contributions, so by making elective deferrals or Roth contributions first, one maximizes the amount of compensation considered for the section 415(c)(1)(B) limit.
I can't imagine any disadvantage to allocating in the way that the calculation is done in Part III of TurboTax's Keogh, SEP and SIMPLE Contribution Worksheet. This worksheet faithfully implements the IRS's worksheet in Chapter 5 of IRS Pub 560, used to calculate the maximum permissible deductible contribution.
Regarding the additional advantage you mentioned, yes, I considered including that in my answer. However, if your net earnings are less than $18,000, you'll need to wait until you know your net earnings before your make the maximum permissible contribution. In my own case, I do as you indicated. I know well before the end of the year that I already have sufficient net earnings to support the maximum permissible elective deferral, so I make those contributions before the end of the year, but I wait until just after year end to make the employer contribution when I know the exact amount of net earnings.
Regarding your follow-up question, yes, you are correct. The contributions, regardless of classification, do not reduce the amount on which self-employment taxes are calculated.
