You also may be able to fund an employer contribution for 2018 - the initial plan year - at some point in 2019 and get the top heavy ratio under 60% (or less). By doing so, the plan may satisfy the top heavy test for both 2018 and 2019 and it can potentially be a cheaper option.
1) If it's not taxable it is not wages and not eligible. So if the traveling salesman submits $7,000 of mileage based on the IRS approved rate under an "accountable plan" that does not mean that he has more eligible compensation (nor should it). The individual is merely incurring legitimate business expenses on behalf of his employer.
2) You mentioned FSA. Those are deductions that reduce taxable income and your document likely specifically says you should add it back (pre=tax deferrals under 125).
I'm assuming you have a calendar year plan established in 2018?
For which the determination date for both the 2018 and 2019 plan year is 12/31/2018.
If your top heavy ratio is more than 60% on 12/31/18 you have a top-heavy minimum required for 2018 (which will most likely be deposited in 2019) and for 2019 which will likely be deposited in 2020.
Not sure what you mean by "beneficiary accounts" - are you saying B and C were A's beneficiaries, and they rolled over their distributions into the same plan? If that's the case, then in my opinion you would treat it as unrelated rollover for purposes of the top heavy determination, although some people have other thoughts on this. See this thread from a few months ago.
I'm not going to claim that this would (or should) ultimately make a difference, but I'm simply curious: was this reported as a distribution and a rollover contribution on the 2015 5500, and was a 1099-R issued?