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Q: 

Is there any difference between setting Layout settings at the template level and the Standard Value level? If you set presentation settings at the template level, does it work the same way it did in 5.2? Is there any advantage to setting things at the template level or is this primarily for backwards compatibility?

A: 

Yes, setting presentation settings at the template level works the same way it did in 5.2.

Yes, setting layout on a template is still supported in 5.3 for backward compatibility reasons.

There are several advantages to setting the layout on the standard values rather than the template, however, including:

1. The layout specified on the standard values is displayed in the item itself, which makes it easier to figure out the layout settings for an item (without having to first open the template).
   
   
2. If you always set layout on standard values, then you can see from the item itself whether layout settings have been set or not. Setting on templates means that you must open the template to find the layout settings.
   
   
3. Layout settings set on the standard values override those set on the template.
   
   
4. All other settings must be set on standard values.  Layout is an exception for backward compatibility, but for new users, this is just confusing.