Looking through the list of Ninjo and Giri.

The Giri list seems OK, and in the RPG setting, Giri (obligation) is pretty easy to get our collective heads around. This will always make for good GM fodder.

Ninjo, this is where the list falls short, some of the items on the list are more Giri than Ninjo.

The way I see it, and as this is Beta, well, everyone has their POV right?

1. Create a secure future with (or for) the one you love
2. Become the greatest sword duelist in the Empire (Not really ninjo, this is almost an expectation or character motivation, or even along the Kensai-style profession)
3. Become the best-known artisan or performer of a certain art (see above)
4. Create a secure future for a particular location or small group of individuals (this holds true under certain conditions)
5. Create a masterful work of art that wins praise across the ages (same as point 2)
6. Take revenge on the family that you blame for the death of someone you loved (Giri, unless the object of revenge is within the same Clan or it is in the Clan's interest for the target to stay alive)
7. Protect a person or group from a particular enemy (yes, and no)
8. Develop a new swordsmithing technique or shugenja invocation (same as pont 2)
10. Uncover lost secrets vital to combating a specific demon or ancient supernatural enemy of your family (giri)
11.Discover your true parentage (very grey area and I think they were looking for items to put in the list)
12. Achieve a particular rank within your clan (see point 2)
13. Become the captain of a ship or the main owner of a particular business (point 2)

I throw at the dearest reader, The Seven Samurai. Not a single one of those warriors had a reason to assist the farmers, or even had a vested interest in the outcome. As we saw in the movie, some samurai/ronin were violently opposed to assisting them as it offered no fortune or glory. It doesn't become the category of ninjo until they arrive and have their first encounter with the village then it may be covered by points 4 and/or 7.

In a sideways comparison, Firefly, the episode where they rob the train. When Mal has the ideal attack of 'Ninjo vs Giri' encounter.

The bond between the PCs ought to be ninjo, and even though they may be different clans, there is a bond tying them together.

Thematically, the classic ninjo vs giri story is Person 1 saves Person 2, then Person 2's Lord demands the head of Person 1. Person 2 will comply with the Lord, then commit seppuku, not comply with the Lord and commit seppuku, or become injured enough that Person 2 cannot fulfill the request (or attempt to look for some other honourable loophole to exploit) and hopefully no one has to commit seppuku.

What ought to be on the list and isn't:

The PCs become honour bound to assist someone, only to find out that they were misled and what they are doing is not so honourable.

alteration to point 11: Discover/uncover the true parentage of Lord/sponsor (especially if the person in question is a truly great leader)

Your argument regarding te second point on the list and all that lead back to that are not entirely correct. They are Ninjo and not Giri, since Giri is about servitude, will those things are about ambition and thus do not happen with the service in mind. Sure, they also can be framed in a service mentality that is required for Giri, but they are supposed to be egostical in nature here.

And I think that is were the setup currently is lacking, to establish the internal conflict between Ninjo and Giri, since it treats both of theose from the game mechanics too independent from each other.

Giri is more than 'obligation', but that's as best as we can get in our modern speech.

Giri isn't just 'Your Lord says to go forth and conquer', or even 'Protect this person'. Those are basic assumptions of duty,

The concepts of Ninjo and Giri are not relatable in English, just as the British phrase 'It's just not cricket' doesn't translate into American.

I am not in any way a scholar of Japanese/Eastern Philosophy and I am happy to be mistaken; I also understand the designers need a game mechanic to fit here to balance against Giri.

I think the game designers will get themselves into trouble (as in tangled in their definitions) if they try and meld traditional real-world terminology into a fantasy setting, albeit one that is based on Japanese/Asian/Oriental culture.