Think about the "unburned diesel, water, oil,soot etc" that you mentioned and then think real carefully about fuel injector failure. Also consider that military and many emergency vehicles don't have that emissions crap installed. Why would that be? Because those vehicles need to be reliable in the case of war or any emergencies.
It's done because they bought credits to omit some items from the engine. In the end, they paid dearly but saved some cash in the form of a less complex engine assembly which requires a little less maintenance. In a fleet, that adds up.
We have this stuff because the government says it's the law. They're not required to have an EGR but the EGR does help the manufacturer meet the government mandated levels of certain gasses that come out of the tail pipe. Does it have consequences? Probably. But I've never seen an EGR fail on a Kubota. Not yet anyway. And they've been out for a while.
They're also not required to have a DPF or SCR system but they do mandate the emission of gasses and particles, and thus far, the DPF and SCR systems are the most economical way to meet those standards. Someone will probably come up with something different someday, will it be better? Time will tell.
On the 1970's and 80's cars and trucks...you can remove the EGR easily. But your fuel mileage goes down (usually). On those, the inert gases that are allowed into the intake stream helps with fuel efficiency among other things. Cars and trucks still use the same principles but the systems that go along with it have come a LONG way since even the early 90's. It it no longer something you take off because the engine will not like it unless other items are addressed at the same time. Specifically the computer programming.
And diesels are a totally different animal when it comes to EGR. Leave it alone. It hasn't been problematic. It's either deal with EGR or deal with Tier IV stuff.