The Meshech Chochma (Parshas Bamidbar 2:17) explains the pasuk - ונסע אוהל מועד מחנה הלוים בתוך המחנות, כאשר יחנו כן יסעו איש על ידו לדגליהם - to contrast the norm of travelling. Kavod is only applicable when people are in their formal settings. but when they are traveling there is no concept of showing kavod - אין מכבדין בדרכים. It is for this reason that the Torah insists that the arrangement of the shevatim around the mishkan be maintained even when they travel. Since the Mishkan traveled within the camp and Hashem's presence was there even at the time of travelling, as the gemara darshens (Menachos 95a) - ונסע אוהל מועד, אע"פ שנסע אוהל מועד הוא ואינו נפסל לחם הפנים ביוצא. Since the Kedusha was maintained even while travelling, it was necessary to maintain their formal formation around the mishkan.
This Meshech Chochma is very difficult in light of the gemaras conclusion that there is really no machlokes about the lechem hapanim and kodshei kodshim becoming passul. The gemara concludes that all agree that at the time of travelling, the מחנה שכינה lost it's kedusha, therefore any lechem hapanim that was off the table, and kodshei kodshim would be passul. However, the lechem hapanim that was actually on the table would not become passul. Rashi explains that the אוהל מועד did NOT retain it's status when they travelled, yet the breads on the table would not become passul based on the pasuk of ולחם התמיד עליו יהיה indicating that so long as they remain on the table, they retain their kedusha. Just as they don't become passul due to לינה, they also don't become passul due to יוצא. The gemara does conclude that there is a machlokes tana'im whether the מחנה לויה ומחנה ישראל also lose their kedusha when they travel, or whether the status of מחנה לויה וישראל remain so that the metzorah and zav are still not permitted to enter their respective camps. It seems strange for the Meshech Chochma to base himself on the drasha that even during the travels the ohel mo'ed retained it's kedusha, since it is rejected at the maskana. It seems that the Meshech Chochma understands like R.E.M. Horowitz who says that when the gemara concludes that the pasuk of ונסע אוהל מועד is for the degalim, it doesn't mean as rashi indicates that אוהל מועד is לאו דוקא. Rather, it means that for degalim we darshen ונסע אוהל מועד -אע"פ שנסע אוהל מועד הוא, but we don't use that drasha to permit kodshim to be eaten since for that we require curtains of the azarah (נראה לי דהכי קאמר, לדגלים קרא גלי שהן בקדושתן, ולא לקדשי קדשים דבעו מחיצת קלעים, ומיושב קושיות תוס' בכמה דוכתי). According to this approach, even in the conclusion of the gemara it maintains it's initial drasha that the מחנות and even the מחנה שכינה retain their kedusha, just that it wouldn't permit the eating of kodshim due to the lack of קלעים.
On a related point (assuming like rashi that the מחנה שכינה didn't retain it's kedusha during the travels) - the gemara says that the issue of the מחנה לויה וישראל retaining their status while they traveled is dependent on the machlokes whether זבין ומצורעין would be chayev misah for entering the azara when the korban pesach is being brought b'tumah. The comparison seems very strange because when the korban pesach is brought b'tumah, the machlokes hinges on whether when we permit tu'mah, we permit all tu'mah. What does this have to do with the issue of whether the camps retain their status during the time of travel? It seems to me that the machlokes between R. Eliezer and the Rabbonon is a very fundamental one. Is the status of the מחנה לויה וישראל dependent on the מחנה שכינה - in other words, is the kedusha of מחנה לויה וישראל an extension of קדושת מחנה שכינה or is their status completely independent of the קדושת מחנה שכינה. R. Eliezer holds that the kedusha status of all the machanos emanates from מחנה שכינה, therefore when a pesach is brought b'tum'ah and we don't treat מחנה שכינה with special status, the status of מחנה לויה וישראל is also lost. The Rabbonon argue and say that the kedusha of the מחנה לויה וישראל is not dependent on מחנה שכינה so that even when the מחנה שכינה is being violated, the מחנה לויה וישראל must be maintained. Similarly, when they traveled in the dessert when all agree that the מחנה שכינה didn't maintain it's status, there is a machlokes whether it is possible for מחנה לויה וישראל to retain their status and not permit זבין ומצורעין to enter the camps, respectively.