But what do you think is the intent of Animal Bonding I and Familiar being on that list..
To me it looks like they are intended for separate target animals.
Familiar is cast on a small creature that acts as the Beastmaster's spy, his/her eyes and ears so to speak. Its small size means it has better chance of sneaking up on a target and listening in unnoticed. Depending how detailed you want to be you could consider the familiar's risk of being hunted by a natural predator.
The familiar spell does not say it can read the animal's thoughts, only that the caster can control the animal and see through its senses. Another spell caster could possibly use a telepathy spell on the familiar while it is being controlled to detect its thoughts.
I'd play it as the Beastmaster can comprehend things such as the scent of another animal detected by the familiar. If the Beastmaster or familiar are acquainted with the animal scent then the Beastmaster will know that the scent belongs to this type of animal and maybe even down to the individual itself.
The bonding spell is for an attack animal or even a mount animal. Once the Beastmaster has gathered their information from the familiar they can then attack from an advantageous position, with the bonded animal charging in first.
As for stacking these spells I can't really see why not if you really want to, the advantage of stacking could be that the familiar would defend a Beastmaster of its own volition.
Familiars are controlled through concentration and may not help the Beastmaster being attacked as their animal instinct to flee might take over and the Beastmaster would be too preoccupied being attacked to concentrate on controlling the familiar's actions.
Being a bonded animal as well as a familiar, they would defend a Beastmaster to uphold the pact they have without the need of concentrated control.
Also it would allow the Beastmaster to spy using the animal as a familiar and if the Beastmaster sees the desired target or opportunity he/she could then immediately order the bonded familiar to attack, the Beastmaster would then be able to break concentration as the attack unfolded.
The downside of stacking would be stacked penalties for the animal's demise.
Spell mastery could be developed with the Familiar spell to increase the size of the animal allowed to further make this 'stacked bonded familiar' more viable.