If you don't want to change the range of travel, spring rates etc etc, then spacing over the top of the struts makes a lot of sense to me. The relationship between the springs, shocks and bumpstops if they have them isn't changed, so should work the same. The spacers just lower the entire strut assemblies down. The geometry change will come from the increased angle at the lower... link is probably the best words for it, but with a 25mm change in ride height, I doubt it will be an issue and might potentially even still be within specification. It's also probably the cheapest way to do it incidentally. Check brake line lengths and link/linkage travel for binding and clearance.
When you get into spring rate changes someone will need to start doing calculations to produce a stiffer spring to which gives increased ride height with the same spring free length. I personally wouldn't run a longer spring with the standard shocks because it will eventually break the shock over time because of the additional load of holding the spring even more captive, and with reduced drop travel it will shock the shock more often as the suspension tops out at full travel.
