The food doesn't actually have to be physically put in the bread. Things that can usually be eaten with bread e.g eggs vegetables are considered no doubt "באים מחמת הסעודה". Apples grapes etc. are practically never eaten with bread so they need their own bracha.
As for certain foods that used to be eaten with bread but nowadays not as much (bananas for example), it's a good question.
As for the role of bircath hamotzi, the Torah gave importance to certain foods e.g bread wine shiv'at haminim, for spiritual and/or symbolic reasons. We could investigate the meaning thereof but must accept it as apriori knowledge - not to come to new conclusions based on our assupmtions.
Consider this theory:
The Torah is well aware that people in different times and cultures eat different food, and despite of that chose certain foods to be important.
Bread is plant-based, processed food - on one hand the core matter is given by HaShem, on the other hand it requires immense human intervention to sow, reap, process, etc.; it requires immense effort to acquire ("לחם" similar to "מלחמה"); whilst animals may eat meat, fruit, the Midrash says that Adam asked HaShem to make his food different from that of other animals, and was thus given bread; it symbolises agriculture, civilisation, as opposed to hunter-gatherer lifestyle;
Throughout the Torah "eating bread" idiomatically means "having a meal". "לחם" means bread, but also the general notion of food (you can check the corcondance);
Therefore, unlike other foods, bread can represent other types of food, which are of lesser importance, that is if they have some connection to it - can be eaten together, as part of a meal - but not if they are completely unrelated, like sweet fruit or candy, or not part of the meal.
This is merely a hypothesis, although it could be further developed, the main point is that understanding this halacha as merely based on bread's popularity in the middle east 2000 years ago, is most likely not the sole explanation, and thus halacha shouldn't be changed acc. to this theory, as much as it shouldn't be changed acc. to any more elaborate theory.