Nice to finally see a second complete plastome of Fagus
I hope you find the resources to generate one of Fagus japonica as well, because that would be the litmus test how good any plastid data can resolve intrageneric relationships in the beeches.
In oaks, we know that they (the plastids) completely fail to resolve species, and sometimes even sections, by being controlled just by geography (there is a Europe-based group that has c. 80 oak plastomes covering the Americas till Asia for quite some time now, but for various reasons, so far haven't managed to publish them). And we see the same pattern in the plastid data assembled so far for beeches. Nevertheless, the comparison here is indeed a great resource for future studies of biogeographic patterns in beeches.
If you can get the hand on material, a most interesting sample would also be the Korean engleriana of Ullung Do in comparison to the currently assembled two beech plastomes. I would not be surprised if it is closer to the Japanese crenata sample than to the Chinese engleriana (although it, by no doubt, is an engleriana, morphologically and nuclear-ITS wise).
For the comparative tree, you may want to add the complete plastome of Quercus rubra, (there are two accessions, one checked ref. genome: NC 020152; and a newer assembly: JX970937), just to cover all major oak (and Fagaceae) lineages so far covered by full plastomes.
You write (l. 130): "The highest nucleotide diversities observed between F. crenata and F. engleriana were higher than observed within other Fagaceae genera including East Asian (Yan et al. 2018) and Mediterranean oaks (Vitelli et al. 2017) consistent with a deep divergence between the chloroplast genomes of the two Fagus subgenera" – since you have assembled the data for your tree anyhow, it should be possible to give actual range (min-max) for these most divergent regions for the included oaks in comparison to the crenata engleriana because they go much beyond the marker set in the cited papers. And maybe add the values for chestnut-Castanopsis pair as well (cf. fig. 2 in our 2016 paper open access, a doodle summarising the fossil evidence and dating/molecular studies for the unfolding of Fagaceae). The latter maybe a better pair to compare to, because these sister genera (one mostly temperate, one subtropical-tropical) may have have split about the same time than the two beech lineages, but are much less diversified than the oaks (where we currently have two subgenera with eight sections, and some 400 species from the marginal tropics to deep into the boreal zone).
Two terminology remarks.
Shen's subgenera, although they make sense, have unfortunately never been properly formalised, so one has to put the name in quotation marks and de-italise them " 'subgenus Engleriana' " instead of " subgenus Engleriana " (the Botanical Code only allows formal genera and infrageneric taxa to be italised; something pointed out to us in earlier papers; I made sure this is correctly done in the 2016 paper, but the proof-setters didn't comply, it should have been " Engleriana lineage " not " Engleriana lineage ")
I would characterise crenata not as "cold temperate" (if you want to generalise) just as "temperate".
It occurs in Cfa (warm temperate, fully humid with hot summers) as accessory element (e.g. Tanega-shima at c. 1000 m a.s.l., island south of Kyushu) to Dfb (boreal, fully humid with warm summers) climates according the Köppen-Geiger classification, e.g. SW Hokkaido below 400 m; data by Maycock, 1994, detailed table can be found as spread-sheet in ES 6 to Grimm & Denk, Rev. Pal. Pal. 172:33–47 (2012) 3MB-zip archive.
Although the climax climate being Cfb, where it is dominant (perhumid, fully temperate with warm summers).
According Trevarthas modification it would be subtropical (sometimes synonymised with "warm temperate", which can be very misleading, because "warm temperate" is also a synomym for "temperate" when recognising a "cold temperate" zone instead of snow/boreal climates, but "warm temperate" was coined and defined by Köppen, where it includes a good part of the subtropics as well) to temperate (= "cold temperate" in some literature, although this usually is used as synomym for fully boreal, conifer-dominated climates) element. This table provides a quick comparison of Köppen-Geiger, Trewartha, and Trewartha-Köppen systems for your orientation. Literature is full of inconsistence regarding climate-vegetation terminology. Best is to choose (and name) one system, and then stick to it (helps also during review, because two reviewers not rarely follow two different concepts).
I hope you'll find the funding to do more down this line.