Let me share my take of the history of Bhutan after due acknowledgement of many tales and write ups from different quarters including official versions and numerous learned individuals. I have been simply trying to reconcile information with events.
1) The 1907 historucal " Genja " is more an oath of allegiance to the new hereditary King by various officials of the time rather than " an agreement " between King Ugyen Wangchuck and the representative of the people of Bhutan. By 1907, most rivals were put to rest or vanguished. And it was also in the interest of British India to have a friendly and stable sovereign Kingdom of Bhutan.
2) The most tale telling part of the allegiance document is the manner it was drafted and the date which reflect the style of British Raj of India. Note the month " December " and " Taari " ( date ) and even the British title " Sir " laboriously recorded down in the document. Very much reflective of foreign draft rather than native and natural. But validity is not only unquestionable, it has been put in full and faithful practice.
These observations are not heresay. The document is well preserved for all to see, read and debate and draw conclusions perspective wise.
However, my following observations of historical events are not based on original documents but simply an honest effort to reconcile events with their reflections out in writings or related by word of mouth from generation to generation. Again just different perspectives and has no bearings of whatsoever since past history is past and holds no relevance to present contexts.
1) Going back to the 1st Desi appointment in 1650 and supposed death or meditation of Zhabdrung Ngawang Namgyal. He is said to have died in 1651 but his death kept secret for some 50 years. Zhabdrung himself could not have wanted his death to be buried that way. He was prepared for such a day. Even if his adopted heir was not of age, he had KhamSum Singye statue built to represent him after his death. In retrospection, the great Zhabdrung Ngawang Namgyal may be the most glorified political tool of the last four centuries of Bhutanese history.
2) The possibility is that Zhabdrung may have been deposed from power from the time of the instalment of the 1st Druk Desi. But Zhabdrung's name and reverrence used to hold onto the power by the 1st and 2nd Desi. Both seem to have died whilst in reign. The 3rd Desi Chogyal Minjur Tempa was so enraged when he discovered that Zhabdrung had long died. He had the 'Machen Lopen' bound and thrown into the Punakha river. So it is safe to assume that though rural people may have been unaware, most officials in administrative and religious centres came to know of Zhabdrung's death in 1667.
3). The Trongsa Penlop Minjur Tempa was appointed the 3rd Druk Desi under the official seal of Zhabdrung. So Minjur Tempa initially believed he was appointed by Zhabdrung himself. In similar manner the 1st and 2nd Desi could also have been appointed by the coterie of inner circles of late Zhabdrung at Punakha Dzong the seat of power. They probably meant well for the nation because they had chosen candidates who had the influence and power base to rule the country.
4) The title of " Chogyal " for Desi Minjur Tempa actually ended the dual system. If the dual system existed then Desi Minjur Tempa could not have been referred to as " Cho- Gyal " Minjur Tempa. In our written history, Zhabdrung is referred to as the Dharma Raja ( the title is foreign which roughly translates to Cho- Gyal ). And he is credited to have establishef the dual system of Desi the political leader and Je Khenpo the spiritual Leader. Zhabdrung was supposed to be the Cho-Gyal the Head of both temporal and spiritual affairs. But one should note that the dual stytem came into being only in 165O just before Zhabdrung banished from public sight. Could he have died earlier ? And his inner circles came up with this convenient system separating temporal power and spiritual power held by Zhabdrung to accommodate the ambitions of powerful religious leaders. Both Desi and Je Khenpo appointees came from the clergy circles and both enjoyed equal powers.
5) It is very possible that Zhadrung was deposed off in 1950 or died and the inner circle used the spiritual isolation practice ( Meditation ) to keep his death secret and rule in the name of Zhabdrung. Their ploy failed when Minjur Tempa after becoming the 3rd Desi, insisted upon receiving audience with the person of Zhabdrung. And when he discovered that Zhabdrung had died, he had the inner coterie punished and the its leader put to death.
6) Lam Ngawang Namgyal did not seem to have believed in his own re-incarnation. Maybe he did not have faith in the process of identifying the incarnate. Anyway, he married with the objective to produce an heir after which he took the oath of celibacy. But his son died of an illness. Then he is said to have identified a young monk Tenzin Rabgye from Drukpa Kuenlay lineage side as his heir. Trongsa Penlop Minjur Tempa raised the heir apparent.
7). In 1687, Desi Cho- Gyal Minjur Tempa suddenly resigned. Hard to tell whether he was forced out by his protege Tenzin Rabgye who was installed as the 4th Desi. Anyway Cho-Gyal Minjur Tempa retired to Tangu-Cheri and died few years later.