The quest "Noises Off" (TR_m1_PT_NoisesOff) in Port Telvannis starts as soon as you hear the latest rumor. I believe this is not up to TR standard, the quest list should only get populated once you actively click on a quest topic (or somesuch).
To follow vanilla style, temples without questlines should have "join the Temple" entries directing you to larger temples (in this case, to Narsis, Ald Iuval and Hlan Oek)
Seems to be a running theme in the Armun Ashlands, NPCs in shan-ahhe generally have mediocore skills/equipment for their level. They're all using exclusively auto-calculated stats. Worst example is "TR_m4_Vraggo the Wrangl" whose only weapon is a spear with a skill of 11 in spear. Same general story for the others.
I killed Jubal Orda in the second quest he showed up in, the one in bodrum, and for some reason he shows up in Ushu-Kur as a non-interactable "dead but not quite" scripted corpse.
TR_m2_tel_guard2 has a low light armor skill compared to the other Telvanni guards. You probably wouldn't notice during normal gameplay, but with mods that increase fUnarmoredBase2 they won't wear most of their armor because they have a higher armor stat without it.
For the same reason, Staron in "Tel Mothrivra, The Glass Goblet" won't wear his shield.
The NPCs in piransulit are all level 15-18, so mid-high level by base morrowind standards which caps out at around 20. But they have stats and gear of low-level enemies. The armun kagoutis outside are more dangerous than them. All of them have auto calc'd stats.
The cave appears related to TR_m7_HH_Sathis4. Based on the NPC scripts they're also related to a bounty quest of some kind. The hostile NPCs within all have auto-calc'd stats. Some specific examples below
TR_m4_O_Vanu: She has the quest related Ebony axe that is very valuable and does a lot of damage, but she has an axe skill of 36.
TR_m4_O_Rathys: He has an Iron great mace and a blunt weapon skill of 14
TR_m4_O_Nalmen: He uses an iron mace and a mix of light and heavy armor. His blunt weapon skill is 36, light armor is 11
Salius Magrodius on the Northern Wind has 2 lines for 'Dwemer ruins', one of which is: "This vessel specializes in supporting Dwemer ruin excavations, but this her first time this far east. 'Northern Wind' was built in Wayrest, and I've spent most of my tenure as her captain investigating sites in Hammerfell for the Society." Jackarn (TR_m1_Jackarn) is actually the captain, and it seems like this line is meant for him.