The latest time to apply word processing and style sequence standards is immediately prior to submitting a manuscript for publication.
Ignoring the word processing standards until the end will result in a considerable detailed editing task. Better by far to follow the standards from the beginning, thus much reducing the final editing overhead.
Applying the style sequence rigorously as you write can get in the way of the creative process. What you do will depend on personal preference. If you use the template, much of the style sequence will be applied automatically. Final adjustments to the style sequence are possibly best left until you are reasonably happy with a chapter.
Given that Writer is better than Word, it's beneficial to adopt Writer sooner rather than later. The option of working in Word and converting to Libre Office at the last minute is probably the worst of both worlds.