This is an interesting topic!
I heard at lot of complain about how the Tama Gb 3 death is way too dark. and now its time to point out where your were wrong.
I wasn't even aware that there was any controversy about Tamagotchi GB 3, or why Tamagotchi GB 3 would be singled out over the other two when they all have pretty downer death-sequences.
The Game Boy games get very little coverage by the community in general, and from what I've seen here on TamaTalk they tend to be rather positively received due to their perceived novelty when compared to better-known releases.
1.Japanese censorship is softer
This is very common on the west that people pointing out thing in japanese media aimed at kids. And why? Its because japanese censhorship is way softer.
This really isn't about censorship, though - it's just about cultural differences.
What's shown in the Tamagotchi Game Boy games
was considered "dark" for an all-ages pet-raising game by Western standards in the 1990s (I was there - things have changed a lot since then), and that is why the first Tamagotchi Game Boy game (which is the only one that made it out of Japan) saw some changes when it was translated into English. This is also why the gravestone death-scene from the original Tamagotchi toys, prior to the Game Boy game, was changed when those came to the West as well (to an angel on the Gen 1, and to a UFO "returning to its home-planet" on the Gen 2) - it wasn't that it wasn't suitable for kids, it's just that kids in one country are raised to see some things as scary when kids in another country aren't, and they wanted their product to have the same wide appeal in its new target-country.
If you don't know what i mean is that other kids games has dark moments even some going pushing to its limit to the its considered PEGI 12 in European country (One of the attacks of Dedede about attempting to eat Kirby with his belly ripped open that has Dark Matter inside of it, in Sa2 An entire level happened because Eggman threatens Sonic if he dosen;t arrive which turn out to be a trap etc).
These examples are really just cartoon/sci-fi tropes, and they wouldn't be out-of-place in a Saturday-morning cartoon - there's nothing especially dark about them. Kirby's Dream Land 3 (and its follow-up, Kirby 64: The Crystal Shards) carries a rating of PEGI 3 (equivalent to an ESRB "E"), and Sonic Adventure 2 Battle currently carries a rating of PEGI 7 (also equivalent to an ESRB "E") with the earlier GameCube release carrying a PEGI 3, and the original Dreamcast release of Sonic Adventure 2 carrying a rating from the older ELSPA system of 3+ - none of these games has ever pushed the limit of being rated a PEGI 12, and any claims of such are just unsubstantiated myths.
I'm surprised that you didn't mention Kirby's Dream Land 3's Zero and Kirby 64's Zero-Two being giant flying eyeballs that appear to bleed when hit, incidentally.
But when considered within the context of those works (context is everything, especially when we're talking about topics like these), that's not especially dark either, since the scenes concerned are dramatic "last stand" boss-fights with distinctly-alien hivemind possession-entities whose nature has been well-established before the player reaches that point, and that's why they carry all-ages ratings.
3.The Tamagotchi not been buried is not innovative
Been not buried is one of the two signs that God hates you and Bandai probably wanted you to believe that you hate your Tamagotchi.
It's most likely that Bandai in Japan doesn't even know about this at all, because the concept of a god as defined by religions that are well-known in the West is actually not on the radar in Japan. I must admit, as a British person, I've never heard of this, either.
Other parts of the world have totally different beliefs about the afterlife than what you may be used to. A couple of examples about traditional Japanese beliefs regarding the afterlife can be found below;
https://yokai.com/meido/
https://yokai.com/jigoku/
They're interesting reading, and I highly recommend checking them out.
