I have some milled heads that are about to go on! They're 0.010" shorter, and I have the thinnest Cometic MLS gaskets, which are about 0.010" thinner. Increasing compression actually is said to be a good idea for stock Gen III M90 setups. The reason is that when you drop a pulley size, you increase heat. Increasing compression effectively lets you have similar power with a larger pulley size, less heat, and therefore more oomph. It puts your M90 into a more efficient RPM range while giving you more power. I actually prefer the idea of increasing compression over dropping pulley size, but it'* a whole lot more expensive and is relatively a more permanent change.
You would have to have the LIM machined as well, yes. If you don't have it machined, it will still fit but the ports won't line up. You'll have some "overbite" and "underbite" on the LIM-to-head ports. Since L36 guys with an extra atmospheric pressure increase top-swap and get about 10 extra horsepower, an L67 engine having its compression increased isn't actually so bad or so risky as long as your tune is good, you have good fueling, and all that other good stuff you have to go with when dropping in pulley size or going to a larger/more efficient supercharger or turbocharger.
Also, you should get shorter pushrods to accommodate the new valvetrain geometry. But as Venom said, no need. And as I might have said, you could just drop in pulley size and tune accordingly.
94 STEi and 99 SLO