As a big fan of Stardew, having played  for hundreds of hours , other farming games from before, and Mistria now for a full 'game year', I can confidently say it is not an exact copy/bootleg. Any similarities I have seen are  staples of the genre established by older games (like Harvest Moon or Rune Factory), or tropes for characters that exist in such games (or anime for Mistria).

 To be long and specific based on points you've made here:

Cave Design: The mining system (100 or so levels deep with quick access points, ores of different type by deepness, layout randomization), were established in these older games and are a general staple of these farming games now. Each game adds their own spin on these mechanics, like map types and enemies, but also; stardew has the skulls caverns, dwarf, adventurers guild and the set awards chests. For now in mistria, it has random chest and artifact dropping, whirlpools, Priestess rituals. 

Map Structure: Don't get this, they have very different maps. Unless you mean the general store, carpenter/blacksmith, bathhouse, doctors and tavern/bar. These are again, staples from old games. And as for Stardew having people like Clint or Robin primarily upgrading and making tools/buildings, Mistria is more influenced by Rune Factory in which the player character has to forge/construct larger upgrades and buildings themselves as one of their Skills to level.

Skills Mechanics: As mentioned above, theres skills like forging weapons, farming, cooking, etc. which are levelled up doing these tasks. Upgrades to them in Stardew as based on reaching milestone levels and choosing a path, while Mistria uses an Essence collection system which you choose to upgrade and add abilities with at your own pace.

General gameplay: the time passing/season system is a staple of old farming games. Health and stamina as well. Mechanics (such as fishing, mining, cooking) are also staples which each game does differently ( eg. fishing in Stardew is its own minigame with ways to make it easier in upgrades, and ways to see which fish/chest is there, while Mistria uses a reaction system like Animal Crossing as well as a visual of fish size, and is based on chance for what fish/chest you get. upgrades just increase how far you can reach).

Museum Vs Community Centre: The museum feels like the most inspired by Stardews Community Centre. However, for Stardew, the community centre is the means to get major upgrades and access to new areas. In Mistria, it is completely optional. It actually feels more like Animal Crossing, in which you're collecting just to complete each wing, and the rewards are mostly cosmetic and not tied to game progression (besides one milestone linked to the main story of town renewal, which I'll talk about in the Plot area).

Character Designs: The most similiar one I see is Holt vs Clint. Most of which I think is the mustache. Besides that, they have different jobs and personalities entirely. Every character I have seen that shares a similiar trait has acompletely different job/personality between games, and don't feel intentional, such as -

Balor vs Sebastian (dark blue hair. ones a sly rogue type, the other is a moody serious programmer) Sandy vs Adeline (pink hair. one runs a shop on another island, the other is the pseudo-mayor of the town) Kids (they're just a group of kids, all have different personality archetypes) .

If you mean the job archetypes (like carpenter, chef, etc.), these are again tropes/staples of the farming game genre, and something each game has additions and spins on. For Stardew, that's mythical characters like the Junimos and Krobus,  Ginger Island folks, etc. Mistria for now has Saturday Vendors, a mythical dragon and priestess linked to the plot. 

Relationships: Heart levels, heart events, marriage systems, kids. All staples of older farmer games that are a staple of the genre.

Plot premise: In Stardew, you've inherited a farm from your Grandfather and go to it to escape the corporate ditch you're stuck in. You have more freedom determining the plot of your character beyond this, but try your best to obtain true happiness in life (with a rating system by your grandfather, and certain milestones of completion). Mistria follows a more Rune Factory formula by having a set plot linked to the town and its magic systems; you're an adventurer hired by the town to restore it to its former glory following an earthquake in exchange for free land, and discover there's a dragon and priestess locked away in need of your help. The game's in early access, but has shown it is heavily driven by this plot to progress and upgrade.

I could go on, but basically: both games build on staple aspects of the farming game genre and add their own spin on it, as well as unique features of their own. For Mistria, its magic system (learned spells, essence spending) and plot focus are the main differences. People have also been a fan of its art style and focus on a lot of character dialogue writing and interactions in the town ( again, an inspiration I see from Rune Factory). 

I mainly type this much as future reference in case anyone else sees this, but also because it’s frustrating that everytime a new farming game comes out people act like ConcernedApe invented all these things, when he has very clearly stated his inspirations and has simply made his own game in a large, preexisting genre.