What did people expect? It's the reason why physical media didn't switch over to SD cards. They still cost more, per the same space.

Surely the cost depends on size of the ROM with Switch being larger than 3DS.  Also there is a setup cost for mask roms.  The unit cost for a 2 million run of Zelda is going to be lower than a 20,000 run or whatever for RiME.  Giving a single figure like $2.50 is made up.

Your $2.0 figure for Blu-Ray replication is also way too high.  Here's just an example $0.75 retail price for 10,000 discs at http://www.quickturnduplication.com/html/blu-ray-duplication-prices.php.  The bulk cost for someone like Sony to replicate discs is a fraction of that.

Where have I heard this before?

I saw this but really don't think it should be an issue..

but since I don't really know how it works exactly, I could be wrong

It's a fact that cartridges are more expensive than blu-rays, but I doubt that it's $10 more expensive. However I understand that the company has to produce lots of copies before selling it, so the developer needs to raise the price to avoid the risk.

That's Nintendo's official policy. PSN has had many occasions of differently priced retail/digital pricing. Vita had 10% off of several digital titles by default.

3DS retail games range from 20 to 40$, with 7 years older technology (so, more expensive per same storage?)
and 3ds games didnt seem to be more expensive just because of using cartridges.

Compared to digital games on mobile, they kinda are, a lot ;)
Yet if you look at games released on 3ds and WiiU, the console version is a lot more expensive. Bigger budget?

Ofcourse Switch games are all cross-buy, console and portable version for one price, so in reality it's a lot cheaper :p

The only way I can see Rime costing more if the publisher is treating the porting costs from Tantalus as extra costs for this version.