Outcome of LaTeX template differs from published papers – should I worry about this?
If you are following the template that the journal has provided, then don't worry about minor differences of this sort.

Journals often have a different post-acceptance "polishing" process for final production, which might involve changing the LaTeX templates or (more likely) converting to an entirely different graphic-design-centric pipeline.  The reason for this is that the review and production are often handled by different staff with different software serving different needs.

Moreover, even if you did do something mildly wrong in your application of formatting, no sane editor will ever say 


  "Muahahaha! You have failed the test of the enlarged first character! YOUR MANUSCRIPT IS UNWORTHY OF REVIEW!


Instead, either the editor will say something like "Your revised manuscript must adhere to XXX format, including the following points" (paraphrasing from one of my published recent manuscripts), or more likely not even say anything because they didn't even notice and only the post-acceptance production staff really care.