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Are there safe places other than inventory to store items such as alchemy ingredients?

Yes.

Most containers reset after you've been away for more than a week (in game time), just like any space on the ground. However there are "permanent" containers, which never reset. They are not indicated in any special way but there is a method to discover them. Any container (usually a shelf) in which you find a quest item is permanent.

For example there is one in the dungeon near Matras, with the skull in it and a plaque beside on the wall. I don't remember any more off the top of my head but maybe others will chime in.

You’ll find one shortly after completing the game on the good ending

in addition Thor Hammer is a safe place to store unnecessary things, I don't remember exactly where it is but somehow a few locations to the left of the city.