I put here the encountered blocking situations with the corresponding bypass thru the console. The post will be updated accordingly.

Reminder : the commands must be preceded by the command DebugMode 1 and followed by the command DebugMode 0.
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When you exit the mine at the Ondolisse Morne, nothing happens. The journal is not updated. (16 Cygni 1)

Status : bug corrected, version 1.01.

You have choosen a Yanni teammate but s/he didn't pop up (16 Cygni 1).
Typo in the convo with the robot.
Near the campfire in the forest, through the console :
rs cy_generate("yti_ranger", 1)
Status : bug corrected, ver 1.04.

You have found Imai and Shino near Yamate but you can't close the quest. The journal is not updated.(16 Cygni 2)
A link is missing in the convo with Shino when only one ronin, Takeshi, is in the party. The following commands will bring back Imai in the party (very important) and set the journal :
rs ga_roster_party_add("imai")
rs sd_debug_quest("q_samurai", 70)
Talk to Gisaku to complete the quest.
Status : bug corrected, ver 1.04.

After you got rid of the bandits, the conversation with Alma ends abruptly. The quests 'Childhood's friend and 'Hot show' can't be completed. (16 Cygni 3)
It actually depends on your teammate's alignment. To advance the journal and to get the deserved XP :
rs sd_debug_quest("q_alma", 60)
rs ga_give_quest_xp("q_alma")
then talk again to Alma.
Statut : corrected, ver 1.02 (romance patch)