MDG:
When someone is engaged in הכנות for tefilo, they are not using an excuse of “getting ready”. Rather, the הכנה is part of the עבודה, and they are in the presence of Hashem. I am not giving anyone a pass for davening late. As much as tefilo is a connection to Hashem, so is living life – if we are doing so in connection. Eating breakfast can be a mundane act, one in which we satisfy our hunger, or a action of seeking energy to be able to get through the first part of the day doing the service of Hashem. This can include anything from learning Torah to working – providing parnosoh to remain connected to Hashem through mitzvos. We can remain connected through many actions that can alternatively be self-serving. While I would hope that הכנות would begin earlier so that tefilo is conducted at the proper time, I still won’t discard actions that are centered around HKB”H with the intent to be closer to him.
What you seem to miss is that HKB”H is present outside of the Beis Hamedrash. As the Rebbe of Kotzk once explained to his talmidim when he asked them where Hashem is, and they tried the lines of מלא כל הארץ כבודו, and לית אתר פנוי מיניה. He responded, “Wherever we let Him in.” If our preparation is with the true goal of Avodas Hashem, His presence exists with us throughout the process.