Crusty, those ghost notes you are calling 'authenitic modelled vintage tone' are rather a symptom of a suboptimal power supply than a likeable feature. Common thing with old amps, where PS capacitors have aged and drifted too much. Ugly sub-harmonics appear the more you drive the amp, that's when your tech should do cap job to take care of that.

BTW, otherwise highly regarded Mojave Amps' early Sidewinder models had the problem fresh from the factory and could be cured by throwing a few dozen more uF at the B+. VOX ACxx amps are known to produce noticeable ghosting by design, that's why you try them all before you buy one (Les Paul anyone...). Old Marshalls often have curable ghosting, as do clones where PS cap values were chosen true to original specs instead of matching them to the non-original iron.

Every tube boffin will agree that prominent ghost notes are indicative of bad design or aging/mismatched components. The sacrilege of ripping out the beloved vintage mystic mojo '54 caps and replacing them with modern age parts is easily outweighed by the fact that after re-capping it you'll have better sound, bass response, s/n ratio and no more ghost notes.

Then again, we are talking about a DSP here, so it may well be an artifact of the algorithms used, Much like a root+5th power chord contains sum and diff frequencies of the original notes, a DSP algo is prone to producing weird (dis-)harmonics, aliasing, and any number of funny side-effects based on input frequency and sample rate ratio.

Given that L6 does not talk about fight club their technology (impulse response? component simulation?) it will remain a mystery whether they sampled (IMO) broken amps or the ghost notes are a by-product of the employed math.

TL;DR I will happily repair and sanitize your tube amp and get rid of ghost notes for good / I personally don't care for authentic reproduction of brokenness and would kill to get my hands on L6's devel software and solder around in the code a bit