I hadn't commented yet but I've read the preprint when was out and I didn't find it a good work. Full of flights of fancy and stretches. As is the style of some geneticists. The truth is that Moots has few samples in hand to draw the conclusions she would like to draw, and mostly from very busy places. So that there were foreigners is yet another discovery of hot water. Take the two non-European foreigners found at Tarquinia who seem to plot with Levantines. They date from the 2nd and 1st centuries BC if I'm not mistaken, when Tarquinia had long since entered the orbit of Rome. Tarquinia was part of southern Etruria, Veio was conquered by the Romans around 396 BC, and much of southern Etruria came under Roman control gradually from 300 BC.
These two individuals cannot provide any information on the origin of the Etruscans, nor on the formation of the Etruscans, at such a late date, nor do they have anything to do likely with the relations with the Punics. The basic idea that every foreign person who died in a place might have helped shape subsequent generations is very weak. But geneticists like it so much because it is a very simple idea, not to say simplistic.
Not to mention that Late Neolithic Morocco is still being used in this paper as a proxy for North African ancestry, when it was the sample that came from a study showing counter-migration during the Neolithic from Iberia to North Africa.
The third dimension is statistically unlikely to change a position significantly in my opinion. In any case the uniparental markers could help us clarify, really strange that they haven't published them anywhere. Hopefully they will when it is published. That there may be Etruscans in Tunisia is very possible, you're right. But there could have been individuals from other peoples, not only the Etruscans. The Punics did not only have relations with the Etruscans, although the genetitsts seem to be obsessed with the Etruscans. According to this preprint out of the 12 samples from Tunisia, 2 end with Italy BA (which I guess is the cluster of samples from Pian Sultano near Cerveteri), 5 end with Sicily/Greece, 4 would be local North African natives, and 1 sample is from sub-Saharan Africa. These published so far are only 6, 50% of the samples from Tunisia. Hopefully, the paper will be improved before it is published.
Yes, it is a surprise, but it may also be due to the smallness of the sample. Here again, it is not at all true what Moots writes that "the contribution of autochthonous North African populations in Carthaginian history is obscured by the use of terms like "Western Phoenicians", and even to an extent, "Punic", in the literature to refer to Carthaginians, as it implies a primarily colonial population and diminishes indigenous involvement in the Carthaginian Empire'"
There are archaeological texts from over 20 years ago that distinguish the Punics and Carthaginians from the Phoenicians and assume that the bulk of the population was local and North African.