The rules for ranger's focus states:
Ranger's Focus (Ex): At 1st level, once per day, the guide can focus on a single enemy within line of sight as a swift action. That creature remains the ranger's focus until it is reduced to 0 or fewer hit points or surrenders, or until the ranger designates a new focus, whichever occurs first. The ranger gains a +2 bonus on attack and damage rolls against the target of his focus. At 5th level, and every five levels thereafter, this bonus increases by +2.
The rules for favored enemy state:
Favored Enemy (Ex): At 1st level, a ranger selects a creature type from the ranger favored enemies table. He gains a +2 bonus on Bluff, Knowledge, Perception, Sense Motive, and Survival checks against creatures of his selected type. Likewise, he gets a +2 bonus on weapon attack and damage rolls against them. A ranger may make Knowledge skill checks untrained when attempting to identify these creatures.
At 5th level and every five levels thereafter (10th, 15th, and 20th level), the ranger may select an additional favored enemy. In addition, at each such interval, the bonus against any one favored enemy (including the one just selected, if so desired) increases by +2.
If the ranger chooses humanoids or outsiders as a favored enemy, he must also choose an associated subtype, as indicated on the table below. (Note that there are other types of humanoid to choose from—those called out specifically on the table below are merely the most common.) If a specific creature falls into more than one category of favored enemy, the ranger's bonuses do not stack; he simply uses whichever bonus is higher.
The abilities are similar, but not exactly the same. By RAW your initial assessment is correct - it would not be allowed. I also looked at many of the ranger archetypes to find out about the ones that replace or modify favored enemy and found that there are very few that replace favored enemy, but many that modify it.
I think you are also correct in stating that this was an oversight. The guide still has an unmodified master hunter ability that states:
Master Hunter (Ex): A ranger of 20th level becomes a master hunter. He can always move at full speed while using Survival to follow tracks without penalty. He can, as a standard action, make a single attack against a favored enemy at his full attack bonus. If the attack hits, the target takes damage normally and must make a Fortitude save or die. The DC of this save is equal to 10 + 1/2 the ranger's level + the ranger's Wisdom modifier. A ranger can choose instead to deal an amount of nonlethal damage equal to the creature's current hit points. A successful save negates this damage. A ranger can use this ability once per day against each favored enemy type he possesses, but not against the same creature more than once in a 24-hour period.
This ability is not modified or replaced by the guide archetype, which also seems to me to suggest that it should apply to the guide's ranger's focus ability, and THAT would also suggest, by RAI, that you could also apply feats (such as Slayer's Knack) to it.
I suppose it all comes down to the needs of your game group and what you want to allow, but it seems reasonable to allow this.