Ok. So, what you're saying is that the option to assign more/less Espionage to a particular civilization (the +/- buttons) is not "How many" points are assigned, but rather a multiplier (of sorts), to show how much Espionage is put into one civilization in comparison to another. Ok. So, increasing them all by 1 point is pointless.
The toggle buttons in the Espionage menu are simply weights. No matter how much or how little EP you are generating, it gets split between your rivals based on the relative weights you set in this menu. If they are all at 0, everyone is evenly weighted, and your EP is evenly distributed if there is enough to do so. If you set weight on one rival to 3 and all the others are at 0, only the 3 gets any EP at all. If you assign weight of 2 to a rival, and 1 to all the others, your EP gets split into half, which one half immediately goes to the 2 weight and the other half is even distributed amongst all the 1 weights. Etc Etc.
This is mostly useful when you are capable of generating a lot EP passively in late game turns (lots of cities w/all the EP buildings) as you can adjust how much EP each rival gets depending on which ones you actually want to accumulate EP on at all, and then weight by how hard they are pumping EPs back on you. For example, you don't really want to waste splitting EPs onto a small or crappy teching AI, as it's not worth seeing what they are teching when they are too slow to matter or worth revolting their cities because you can push them over easily. Likewise there is often little point in EP focusing a vassal, as they often give their tech to their master anyway. That can occasionally work out if it's one of the small good teching guys (Pacal, Huayna, Ghandi, etc) who got capped and hates his master a lot, as the vassals don't actually HAVE to trade their tech compared to how Masters often just gift it away to their vassals regardless.
EP distribution always use integers and is applied in the order in the list of rivals in the Espionage screen, so if you only have +4EP a turn and 6 rivals with even weighting between all of them, that four EP gets split into +1EP for the first 4 rivals listed, and nothing to the last two. This is why they tell you to assign a weight to "target" your EP at a single rival, because as you meet them and you leave the weights on default 0, it splits up and becomes useless as it's not enough to do anything with.
The most typical use of passive EP is to see the tech they are working on, which requires you to be close in EP ratio to maintain in the long term. You'll never keep up with just +4EP passively if you split it up, as almost any AI is likely to devote some EPs back on you as well, and they start to generate more EPs than you with buildings and running their EP slider. Honestly, I don't even really do that anymore, as it's largely only useful before Alphabet (you can always figure out their exact tech standing if you are close enough to them in tech using the trade info) and because of known tendencies of the AI tech preferences in this stage -- as an example, yeah, you know on Immortal they pretty much ALL are gonna go Iron Working, Math, HBR and maybe Currency or CoL with a lot of likelihood by the time you get around to being able to make a tech trade for Alpha, but much less likely to Aesthetics, Compass or Metal Casting by then even though they are right around the same time in the tech tree.
Later on in the game, when you are generating more EP or get a lot of it quickly (Great Spy or running the slider) you can use Espionage Missions to revolt cities during attacks, steal techs, or do other cheekier things like force a civic/religion swap. It isn't very practical or effective to do much else unless you are doing something very specific (such as Spread Culture to help flips, or sabotaging a Wonder you know is nearing completion in a specific city)>
And why do the cost of certain Espionage related activities increase?
Rising costs of techs in beakers, rising cost of builds in hammers, modifiers imposed by things like different/same religion, and most significantly, because the AIs accumulate EPs back on you, which makes everything more expensive the worse your ratio of EPs on them is to their EP on you. And AIs start to generate A LOT of EP when big or in the late game.