(a) The Pischei Teshuvah (Yoreh De'ah 289:2) records the Minhag of the Vilna Ga'on not to wrap the Mezuzah, due to the concern for Chatzitzah. However, the Maharam Shik (Yoreh De'ah 288) offers explanations for our Minhag to place the Mezuzah in a casing. One of his explanations is the rationale that whatever is used for protection is not considered a Chatzitzah, and is Batel to the Mezuzah.

(b) The two Minhagim regarding the order of the Tefilin predates Rashi and Rabeinu Tam by hundreds of years (see Tosfos), and is alluded to in the Zohar. (Apparently both were used in different communities, at the time of Rabeinu Tam and Rashi -MK)

D. Zupnik

It is true that it has been said in the name of the Vilna Ga'on not to wrap the Mezuzah -- and that some Briskers nowadays simply nail it in place under a piece of parchment, to satisfy this opinion. However, the ARUCH HA'SHULCHAN (Siman 289) and CHAZON ISH both write that whoever cited the Ga'on on this matter, must have misunderstood what the Ga'on said. He cannot have written that it is a Chatzitzah which disqualifies the Mezuzah, since the Gemara (Bava Metzia top of 102a) says that it may be placed inside a bamboo tube. The Chayei Adam (a close disciple and relative of the Ga'on) also seems to be of the opinion that a Mezuzah may be wrapped, since he discusses (in Hilchos Tzeniyus) double wrapping the Mezuzah.

One might argue that the Vilna Ga'on only opposed a wrapper that is not secured to the wall of the house, such as a plastic bag (or piece of leather). The bamboo tube was nailed to the wall, so it was not considered a Chatzitzah, but rather part of the wall itself. Others point out, however, that if this argument is true, it would be necessary to *first* secure the tube to the wall, and only then to insert the Mezuzah, in order to avoid the problem of Ta'aseh v'Lo Min he'Asuy.

M. Kornfeld, based on a discussion with Rav Eliyahu Feldman