I am aware of this paper ( Sci Rep . 2014; 4: 3746, Molecular detection of Lactobacillus species in the neovagina of male-to-female transsexual women ). That was not actually the conclusion of the study. The purpose of the study was to examine the general opinion that penile skin lined neovaginas are not able to support the growth of lactobacilli. They found that Lactobacillus species were detectable in 47/63 transsexual women (75%). Thus, the take home message was "if you look hard enough, you can indeed find some".

"More than 90% of women harboured a combination of two or more neovaginal Lactobacillus species. In this study we report the frequent occurrence of lactobacilli from neovagina of transsexual women. Both, frequency and composition were similar to the normal lactic acid bacterial microflora in both women of reproductive age and postmenopausal women." (emphasis mine)

In other words, the occurrence and diversity of lactobacilli were similar to cis-vaginas. It says nothing about the relative amount of lactobacilli. In fact, one could infer that amount is small because the authors make a point that the PCR technique is sensitive enough that it can find species that were unculturable or undetectable by other means.

A better study to read is Microbiome volume 8 , Article number: 61 (2020), The neovaginal microbiome of transgender women post-gender reassignment surgery . This study examined the metaproteomics of secretions collected from the neovaginas ( n = 5) and rectums ( n = 7) of trans women surgically reassigned via penile inversion/scrotal graft with ( n = 1) or without ( n = 4) a sigmoid colon graft extension and compared with secretions from cis vaginas ( n = 32).

They found, on average, the most prevalent taxa by protein abundance in the neovaginal samples were Porphyromonas (30.2%), Peptostreptococcus (9.2%), Prevotella (9.0%), and Mobiluncus (8.0%), with a large proportion undistinguishable (16.9%). In cis vaginal secretions, the most abundant taxa were Lactobacillus (64.8%), Gardnerella (18.2%), Lysinibacillus (8.2%), and Prevotella (2.7%)

Their conclusion was that neovaginal bacterial composition is more similar to that of non- Lactobacillus -dominant (nLD)/polymicrobial than Lactobacillus -dominant (LD) cis vaginas .

I believe all types can go through metaplasia.

There aren't a lot of studies on this, but it doesn't look like keratinized skin undergoes any significant cytological change (Ann. Plast. Surg. 2007 Nov;59(5):546-9, Do histologic changes in the skin-lined neovagina of male-to-female transsexuals really occur? )

Here is the abstract:

"Controversy exists on whether or not the epidermal keratinizing squamous epithelium of skin grafts and flaps applied to line a neovagina changes histologically to a nonkeratinizing mucosal type squamous epithelium after vaginoplasty in male-to-female transsexuals. To end this discussion, the aim of this study was to objectify the short-term and long-term histologic aspect of this neovaginal epithelial lining. Biopsies were taken from the epithelium lining of the neovagina of 9 male-to-female transsexuals, from the moment of vaginoplasty up to 14 years after. These were stained with hematoxylin-eosin and periodic acid-Schiff stain for histologic comparison to normal vaginal biopsies. Because no changes that might have been induced by local influences or hormonal therapy were found, we concluded that short-term and long-term changes in the histologic aspect of inverted skin flaps do not occur after penile and scrotal skin vaginoplasty in male-to-female transsexuals."

There is a later paper ( Cytopathology 2017;28:184–191, Cytology of the neovagina in transgender women and individuals with congenital or acquired absence of a natural vagina) which is not much more encouraging:

"The cytological findings of bowel and (penile) skin-lined neovaginas in patients with gender dysphoria (GD) and in individuals with a congenital or acquired absence of a natural vagina resembled the cytology of the normal vagina in only 10%. Sigmoid-derived neovaginas demonstrated special cytomorphology with a predominance of degenerated columnar cells. Abnormalities of squamous cells were found in 25% of patients, emphasizing the need for patients with neovaginas to engage in cancer screening programmes."

So basically your odds of getting cancer are greater than metaplasia.

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I do have mucosal secretions

I do too, but it seems to come from the urethral tissue used to make my labia minora. I never really noticed any increase in wetness down there after getting a peritoneal graft, but gad I get gooshy wet upon arousal now when I play with myself. Weird.