The hippogriff companion is not levelling up with the master nor does it level up with boon companion whether the master has taken other class levels or not.
I still dont think other aspects are working right. I start with a 1st level ranger, add the archetype, add 1 level, select archery combat style and monstrous mount bonus feat. Now he can select a hippogriff as an animal companion. Now add two more levels, so ranger 4th level. The Hunter's Bond class feature should be blocked. Notice the last sentence of this paragraph:
Hippogriff Companion: At 2nd level, a Sable Company marine adds Monstrous Mount (see page 14) to the list of bonus feats made available to him by his chosen combat style, regardless of the style chosen. He can only use this feat to select a hippogriff mount (see page 14). If he does so, he treats his ranger level – 1 as his effective druid level. A marine who takes this option does not gain the hunter’s bond class feature at 4th level.
So, – IF – a Sable Company Marine ranger takes the Mostrous Companion feat as a bonus feat, he can only take Hippogriff as his Ranger animal companion from that point forward. Later at 4th level he doesn't get hunter's bond and therefore cannot select from any other animal companions or hunting companions.
There are also secondary consequences of the hunter's bond issue... The archetype is not REQUIRED to take the feat at second level. And if he doesn't he doesn't lose Hunter's Bond class feature. But if he takes the Mostrous Companion feat as his level 6 bonus feat, he immediatley looses his hunter's bons class feature and his regular animal companion which must be replaced with a hippogriff animal companion.
I'm guessing the easiest way to block the hunter's bond class feature in both cases (since adoption is optional) is for the monstrous companion feat chosen as a bonus feat to also add an automatic selection to hunter's bond and decrement the number of choices so that any PC that has already chosen a hunters bond has a "too many hunter's bond selections" notice to resolve.