If your AutoText has a paragraph mark included, it will carry formatting.

If the formatting is directly applied (not through styles) it will carry into the new document.

If it is through styles and the styles have not already been used in the new document, the style definitions from the AutoText entry will come into the new document.

When you are doing work like this, you want all of your formatting, in both the AutoText and your document templates to be done using styles.

Understanding Styles in Microsoft Word