Adding another food that can be vinegar pickled will not change the safety of the recipe- so no issue with adding the pepper. However the size of pieces does matter for food safety, because the more gel-like the food is the harder it is for heat to penetrate. (I learned this in Culinary Arts College)
"If the food is thick, puréed, or mashed; if there are large pieces of food in the jar; or, if the food is packed in too tightly, heat penetration can be slower than in more liquid or loosely packed foods. If a specific heat process is not calculated for each food and style of pack, the heating may not be adequate, and the food will be underprocessed." -
-source
The standard accepted safe work around for this is to can it exactly as directed, and then blend it all when you open the jar to use it. Since unsafe home canned food can kill you, I always go with the approved safe way , even though I'm a kitchen rebel who almost never follows a recipe in any other situation.
Alternately, you can puree it and *not* can it, but instead cook it in a pan and store it in the fridge if you intend to use it in the next couple of weeks.