Breakfast foods come pre-packaged, so there is no way to add extra bacon or substitute a different bread.
Bacon or Sausage (or the Impossible Sausage) sandwiches can be made without the meat, egg, or cheese. Just ask.
The Ick Factor
Breakfast sandwiches with bacon (Bacon-Gouda-Egg and Double-Smoked Bacon) often have chewy bacon that seems undercooked. Even worse, they all (including the Spinach Feta Wrap and Bacon-Sausage Wrap) sometimes have cold spots. This can be the result of not having been fully defrosted. You have a few options though (listed from worst to best)....
Most pastries can be served warmed or room temperature. Items with frosting - including the Iced Lemon Loaf, seasonal frosted cakes, and cake pops - cannot be warmed.
Cake Pops
Two of the standard cake pops - the Chocolate and Cookies and Cream ones - have a chocolate cake inside.
The other standard one - the pink one known as the Birthday Cake Pop - has a white cake inside.
There is always a seasonal one. It might be a Bee, an Owl, a Bunny Rabbit, or whatever. It has white cake inside. Many of the seasonal ones - whether an owl, a frog, or a giraffe - you can ask for the kittycat one because they're all shaped like a kittycat.
Even the Bumblebee Cake Pop looks more like a kittycat than a bee. And any barista working drive-thru has plenty of first-hand knowledge of bees.
Bagels
Yes... Starbucks has bagels. But you know there's a Panera just across the parking lot, right?
Sandwiches you grab from the refrigerated section by the cash registers are warmed by default. You can request that it not be warmed if you want it cold or plan to eat it later.
Make sure to eat a protein box within a day or two after you buy it. They can go bad after a few days, even if you keep them refrigerated.