I installed a new stem with different height to the previous one and now would have to place two spacers above it to make it adjustable. As the stem is clamping full height to the steerer tube I think this is probably ok or am I missing something? Wouldn't be a problem to order another properly sized spacer, I just don't have it here and would live with it if it's no problem.
You can have as many spacers above the steerer as you need to raise the top-cap off the end of the steerer.
Ideally you'd buy a single thicker spacer, but stacking up several would work too. Put the widest one on top, directly under the cap so it overlaps more.
If you think the steerer is too long, it can be trimmed but that limits your options for future changes.