Geometry Nodes: Realize instances when applying modifiers

The fact that geometry from instnances isn't realized when applying
a nodes modifier can be very confusing, especially for new users.
Nodes themselves realize geometry instances implicitly whenever they
need to. We also currently make instances real and convert points to
mesh when a modifier is added after the nodes modifier. With this
commit, we simply do the same thing when applying the modifier.

There are a few downsides though:
 - This can be an extremely heavy operations in some cases where
   geometry nodes is used to instance heavy geometry.
 - We will still have the issues with materials, since instances use
   materials from their original objects, but real geometry uses
   materials from the modifier object.

It was decided to live with the potential performance downsides
for now, the idea is the upsides of the change are more important,
and people making complicated setups will be more likely to know not
to apply the modifier. In the future there could be a warning if it's
necessary though.

Ref T87083

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