They aren't, you are just going through a "visa agency" which really is just paying someone to do the visa application process.
You can easily do this yourself, or go in person. The reason you pay select visa agencies is so they can expedite the process, or in certain cases expeditate through some sort of kickback or knowing someone within immigration. This can be as simple as a firm reserving all known slots for the future, to having an insider who can selectively pick your application, put you on the top and process you as needed.
If your visa firm doesn't have any "information" then you aren't paying the right firm and you are just wasting your money/time on a process you most likely can do yourself.
Not all visas require your passport, many countries will happily just take your biometric page and apply a sticker upon entry that is for long term stay/non tourism. There are also different organizations like schools/universities that will do this entire process for you as they act as your "visa firm."
It takes a long time because every country has inward demand, the immigration process is designed to be a bottleneck to slow down, verify and selectively give out visa to people who are deemed "worthy of it."
1. You are forgetting that countries have the right to refuse entry to anyone they don't seem fit. It does not matter if your time, money or other intangible or tangible item is at stake.
2. Many countries do have completely electronic processes, China's/PRC has an complete online procedure for a 10yr tourist visa. Taiwan has a complete online election for a 5 year gold card program that is workervisa/residency/permenant residency. Japan allows completely online transactions if you are sponsored by a university or job. Thailand has a complete online process for tourism and business via Thailand pass, Cambodia is purely electronic conducted over email.
There does not need to be a physical visa in your passport, Indonesia ITAS does not give you a unique visa or such, but the reason why you have a physical sticker instead of other paperwork is because it serves as your identity paperwork in that country, which you can use to get a tax number, open bank accounts and conduct business all in one.
You seem to have a general misunderstanding of how these visas and their processing works, and that's okay - it is a system that is paperwork based and is bureaucratic in nature, on purpose. That's what it is, and that's how it serves - to create an anchor in confirming your identity.