"In particular, algebraic effects are combined seamlessly, whereas monad transformers are needed in the monadic style." Implies otherwise...but to be frank, I don't care. As long as I can get these features without type pollution (as monads do in Haskell) then I'm happy.
My point is that category theory is useful for discovering nice abstractions such as algebraic effects and handlers or Monads for that matter. It's like all math, just a clever way to write/solve problems...
As for the semantics of algebraic effects and handlers, if you are not really interested I won't bore you with a long winded explanation. Suffice it to say that you can get the advantages of Eff in Haskell by using free Monads (the syntax of Eff is nicer though).
Monads and monad transformers are different things, of course. However, it's all really quite doable in Haskell. There's two main reasons it's _not_ done, though: a) effect style isn't so great when the effects don't commute b) it's slower.
If someone ever cracks the speed thing, I bet you'll see a lot more Haskell with Eff monads in it.
We can look at effects as a dsl built upon a monad. The state effect lets us get and put state, for instance. There are two extensible ways to represent this:
data State a self = Get self | Put a self
class State repr where
get :: repr a
put :: a -> repr ()
With the first implementation we write a function that interprets the adt, writing different interpreters is easy. We parametrized over self so we can combine languages by combining their adt's and give that as self. To tie the knot we use use recursion and end up with the free monad.
With the second version we depend on multiple type classes to combine languages and implement them for different types to get different interpreters. The big advantage with this approach is that we don't have to construct the adt's before interpreting which is where the speed difference comes from.
Tl;dr: if you want to go fast you have to skip constructing adts and if you do that you end up with something like haskell's mtl.