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Yes I've had that experience and a similar one once the first ARM SBCs came to the market circa 2009 with the SheevaPlug. At that time was trying to get stuff work on those and I know how things go.
After this point you're essentially saying the same thing I was BUT replacing the word Javascript with Java/dotnet. Once those virtual machines runs well on ARM (as they mostly do) developers won't care anymore about the architecture. I only picked Javascript/Typescript as an example because it will most like take over everything in a few years.
And why are they trying to push developers into ARM? It is medium term strategic investment, they're just waiting and pushing ARM manufacturers such as Ampere Computing to develop "bigger and better" CPUs that will take on Intel. Once they're very competitive in performance they'll simply start replacing Intel with ARM and nobody will complain because at that point the 90% of developers are using Java/dotnet/Javascript (things that run on VMs) will not even notice the difference between running on their amd64 or ARM.
It seems that Facebook, the holy grail of running PHP, doesn't agree with you. They've been pushing ARM on their datacenters for years now.
They need to get competitive in performance first, and they haven't been for a few decades now.
Even still, developers will know, because their Docker images suddenly stop working. I'd agree with you for shared hosting setups, in the manner PHP hosts and a select few Python hosts will allow you to upload files onto a shared server and run them.
Even in devops environments, I'm pretty sure nobody is actually juggling raw source files around the servers. Everything is getting neatly pipelined, and those pipelines need to be changed or the code will simply break.
I don't know what PHP is doing in their datacenters, but Facebook is not exactly a nornal software company. Their open server architecture is pretty neat but I don't think they influence any companies but their own in their push for ARM.
All of that said, I agree that architecture shouldn't be a problem in practice. If you're a programmer and you don't know the difference between ARM and amd64, you're going to run into much bigger problems than "something is up with my build". In practice, though, I expect Linus to be right, and that ARM will remain a niche product for at least the foreseeable future unless Ampere manages to pull off the stuff they've been promising for years.
There's one exception, though: small, new IoT startups are moving to a very Raspberry Pi-based ecosystem, to the point of devices literally including full Raspberry Pis. Intel seems to be losing the "small computer but not microcontroller" market pretty badly.