@IntuitRebecca   You pretty much nailed it.

Setting aside any EFT/WebPay scenarios - I think the disconnect here is that Lacerte generates the full amount of PTE on line 35, unless it's overridden.

I've explained to "Kenneth" in multiple emails that the amount on Form 3804 Line 1 amount should flow to Line 29, not Line 35, of 100S, but he and I were on very different wavelengths.

RE: The 3893 (PMT) should generate with the full amount from line 35 (or, line 35 less any amount entered as "Pre-payment already made") .

Yes. 

RE: It sounds like you're expecting line 35 to be $0 when the client hasn't paid any PTE yet; so you use the PTE Elective Tax Payment Vouchers(s) override to set that line to zero, but then you're stuck with no voucher or instructions. Is that correct?

Yes.  My comment was based on the same logic of how tax, estimated tax and tax balance work.  On Form 100S without electing the PTE Elective Tax , a balance on line 40 should generate Form 3586 (e-file) .  In the 2020 program, that was how it worked. 

A bonus while we're at it.  I just checked the 2021 program, (again, in this case, zero on Line 29 and Line 35, i.e. PTE Tax NOT involved).  Form 3586 (e-file) is NOT generated for an e-file 100S that has a balance due.  Probably a domino effect of the above.

Sigh....