First, understand that waypoint activation fields are not executed until a group reaches the waypoint radius and conditions met, so even with the waypoint set to true and the waypoint activated(group completing the waypoint preceding it), unless the group has entered the radius, the waypoint will never complete, thus any code from the condition field down will not execute.
So, if something prevents that group from reaching the waypoint, the code never executes and the victory condition is never met.
Regarding the waypoint "Type", there is no such type as "Combat", that is a behaviour state. SAD would certainly imply Search and Destroy as that is the only "Type" close to the acronym. Search and Destroy adds 3 or more invisible waypoints to each waypoint with this type so that once the group enters the radius, rather then complete as a normal Move waypoint would, the group moves through a series of random waypoints assigned to it upon entering the initial waypoint radius and when all invisble waypoints have been reached, the initial waypoint condition is met, thus completing the waypoint and executing the code below the condition field.
So, once the groups attached to those waypoints reach the particular waypoint with the victory condition and have satisfied the conditional requirements, the victory condition would be met. Which in your case, objective 3 status would become complete and a global variable "VictoryCondition3" would be declared true(1), which is probably then checked by a later script for status to determine compliance of another condition.
Regarding Seized by side activation, The determining factor for condition compliance is side to side unit ratio. If the same number of side a is equal to side b, the condition will not necessarily be met,(not necessarily because other computations may factor into the condition such as weapon type, unit type, rank, skill level, etc.).
It is safe to say that if the number of Independent units, significantly outnumber the opposing force, the condition in this case would be satisfied. But bare in mind that the calculations may depend highly on skill level and rank, so that if three highly trained, highly ranked combatants engage 12 lowly skilled, lowly ranked combatants, the ratio for compliance would change.
In other words, objective 3 can be completed by those groups completing the mentioned waypoints OR by the Independent force dominating the mentioned trigger area.