Yes, the language is confusing. And the button talks about a non-action (‘keeping’ meaning not changing the selected glyphs). Perhaps better the other way around:
- window title: ‘Update Auto-Alignment’
- ‘The following changes will be made to aligned components:’
- ticked = apply change, unticked = leave as is
- text below: ‘Component positions will be updated in selected glyphs.’
- button: ‘Apply’