If you go with too high lift or bad lobe separation (causing the intake valves to collide with the exhaust valves) then you can have some serious issues from pistons contacting valves. Oversized valves might require pistons with larger valve reliefs to prevent contacting the valves. Milling the head to gain some CR may also affect piston to valve clearances. Other than the cam timing and valve to piston clearance, you should not have ANY issues with the engine from most common mods to the head (including cam changes). Just make extra-sure that your cam timing is set properly for your setup (meaning you will need adjustable cam gears).
I believe what you've heard refers to the problems with the "floating" bores in the engine. They're a real hotspot when it comes to putting a good amount of boost, increasing the CR of the engine, or elongating the stroke since they tend to flex. When that happens you can wind up with all kinds of issues.