"בשלושה דברים ניתנה התורה: במדבר, באש, ובמים"
What is the message of the Torah being given in the desert? If we have the midbar mentality (relying on God in the absence of any resources) then Torah is given to us as a gift.
Since Dan was large (62,700) they travelled last and were the מאסף לכל המחנות. Rav Chatzkel Levenstein compares Dan and Binyamin - When the tribes went down to Mitzrayim Dan had 1 child who was deaf whereas Binyamin had 10 children. When they departed Egypt Dan Had double the number of Binyamin! God is in charge.
Rav Hanan Porat on the opposite connotations of חומש הפקודים vs. במדבר: the desert represents disorder and hefkerut; counting is the epitome of order.
Chida: Why Gad merited to have Moshe buried in its territory and the greatness of being מוותר.
Why was there a need for flags?