Does lightning record page overrides the standard page layout in salesforce? Updates on the standard page layout seems to not taking effect if lightning record page is active. How are fields' FLS configured on Lightning record page?
Page Layouts govern the Record Detail component on the Lightning Record Page, if present. They also govern the presentation of Related Lists and which fields and buttons are shown there.
Additionally, Page Layouts and Compact Layouts govern the fields present in the highlights panel (if present) and the Quick Actions available as buttons or as publisher.
So neither really overrides the other: Page Layouts and Lightning Record Pages work together. However, if the Lightning Record Page does not show a Record Detail component, much of what you'd expect from the Page Layout won't be visible. If you don't see changes you expect, it's possible you do not have the correct Page Layout assigned to the current user profile and record type.
FLS is not configured on Lightning Record Pages or on Page Layouts. Page Layouts may mark a field read only, but this applies only to interaction with that specific layout. FLS is configured in Profiles and Permission Sets.