FamilySearch doesn't seem to recognize the difference, as far as indexing input is concerned.
As an indexer I have always added a period when it was included in the image I was indexing. When I started reviewing other indexers' work I noticed that people seem to leave them off more often than not. At first I was concerned about this and would go back and "correct" it to mirror more accurately what the source document showed, but have since stopped because FamilySearch doesn't seem to recognize the difference. I say this because if I correct an indexer's typo from "Chalres" to "Charles", for example, it shows a red arrow in the box as an option to revert to what the indexer originally input. However, if I add a period after an initial that was missing one, that red arrow does not appear - as if I had made no changes to what was originally input by the indexer.