All D&D 3.5 sources agree that incorporeal creatures can only enter a solid object shallowly.
The question of which sourcebooks take precedence is very noodly and technical, and rarely entertained except as a forum topic. According to the D&D 3.5 Dungeon Master's Guide p.6, "Adjudicating", the DM has ultimate authority in adjudicating rules. In the case of rules contradictions, the DM is advised to pick whichever they think is best and stick with it. That's the official rule.
However, in the specific case of the rule that incorporeal creatures who enter a solid object must remain adjacent to its exterior, all D&D 3.5 sourcebooks agree that this is the rule. The omission of this rule from the Epic Level Handbook (a D&D 3.0 book) reflects its omission from the D&D 3.0 rules in general, not a unique ability of this class to ignore the restriction. The perfect wight's Incorporeal quality is merely a copy of the standard Incorporeal rule from the 3.0 Monster Manual, which would not apply in a D&D 3.5 game.
Rules of precedence
Since the question is tagged dnd-3.5e, it's a reasonable assumption that you're playing D&D 3.5. According to D&D v3.5 Accessory Update PDF, using 3.0 books in 3.5 is entirely valid. However, you're still playing by the D&D 3.5 rules.
The D&D 3.5 Dungeon Master's Guide errata document asserts that primary sources take precedence. The Monster Manual is explicitly stated here to be the primary source on supernatural abilities, which includes Incorporeal.
The Monster Manual p.310-311 defines that:
An incorporeal creature can enter or pass through solid objects, but must remain adjacent to the object's exterior, and so cannot pass entirely through an object whose space is larger than its own.
There is some debate over whether the Rules Compendium supercedes the Monster Manual, but it's a moot point in this case, since the Rules Compendium also reflect this rule.
The description of Incorporeal quality in the perfect wight's entry in the Epic Level Handbook is a direct copy of the description of the Incorporeal quality in the D&D 3.0 Monster Manual, with the only changes being "she" instead of "it", "the perfect wight" instead of "the creature", and a clarification that the perfect wight only loses her Strength score while incorporeal.
In other words, the perfect wight's description of Incorporeal is merely a statement of the rules for incorporeality in general in that edition, not a unique definition that this class should possess some special form of incorporeality. Since you're playing D&D 3.5, the D&D 3.5 rules for incorporeal creatures apply instead.
In the general case
The Rules Compendium p.5, "Order of Rules Application", asserts that a specific rule overrides a general rule, such as a monster statblock overriding general monster rules. While this does allow for the possibility of a prestige class having a unique form of a common ability, in this specific case it's clear that the perfect wight's incorporeality is intended to be standard incorporeality. The 3.0 Monster Manual would have given the sought-after freedom, but only if you were playing D&D 3.0.
In the general case, it goes back to the already-explored question of the precedence of sources, and the debate over whether Rules Compendium overrides the 3.5 Monster Manual and/or its later reprint. Monster Manual III probably does not specifically supercede Monster Manual's glossary, although many DMs would use it as such. The differences between MM and MMIII, aside from a few small clarifications, are that items held by an incorporeal creature are incorporeal until they drop it, incorporeal melee weapons suffer the same miss chance against corporeal creatures as the reverse, and nondamaging spells which do not need to target a body affect an incorporeal creature normally.