Let me tackle this one.
If you are baking a loaf of bread,, it takes a little time for the oven heat to reach the center of loaf. Factors, may be oven baking temperature,, and baking time.
Lower temperature means longer bake time.
So If you are following a Bake time schedule, sometimes things may be off.
If you are viewing, and think loaf looks tanned enough, you can be tricked into thinking its baked all the way through.
Solution;
Use a thermometer, and when interior temperature reaches 190 to 205°F, bread is totally baked.
Now to the Focaccia; If you are using sourdough, maybe you don't allow to get second rise sufficiently, and result, may be a collapsed dough, since it gets loaded on top with delicious ingredients.

Focaccia being thin should bake all the way thru easily.
I make my focaccia using yeast. Always had success. I may have posted recipe here, so it may be in the index.
Below is a picture when I checked my yeast raised coffee cake.
Bread follows same rules. That cake is in a common bread pan.
Temp reads 208°F
View attachment 4220257
Pebbles,,, Here is a tip I often use when I bake bread. I somewhat cheat,, since I usually have a quantity of whey from my cheese making adventures. I freeze about 2 cup portions in plastic baggies for future use. I use yeast though.
So I use the whey
as part of my liquid ingredient.
So I know you have kefir adventures. Consider using the not so desirable kefir to your liking, (sour), in Baking a Yeast raised loaf of bread.
Experiment.
The sour, will give sourdough flavor. Cheat imitation.

The milk portion will give bread soft texture.