In these sentences
Once the objectives of the project were determined, the initiation stage was completed. Therefore the work could have been directed to planning the execution.
does the phrase "could have been..." indicate that the aforementioned enabled the work to be taken to planning the execution (which may or may not have followed) or it was possible but didn't take place?
That's not past continuous. It's modal + passive form of past perfect.
And to your real question, it is ambiguous with only this context. A modal is used to compare possibilities, and if only one case is described, the other is assumed.
These two sentences could answer two different questions.
Why were people billing time when the initiation stage was over and the execution stage had not yet started?
Why did people stop working at the end of the initiation stage?
In the first case, the condition contrasted by the modal would be the expectation that nobody bills time when there is not an active phase of the project.
In the second case, the condition contrasted by the modal would be the expectation that people make use of the time available to plan for the next stage.
Once the objectives of the project were determined, the initiation stage was completed. Therefore the work could have been directed to planning the execution.
is written very awkwardly but essentially means
The establishment of the project's objectives ended its initiation stage. It then became possible to do something.
The expression "directed to planning the execution" isn't comprehensible English and it's unclear whether "the project" and "the work" are supposed to be the same thing or two separate things.
Luckily, it is so ungrammatical that there's only one other place on the internet it's ever appeared. Presumably, the similarity in usernames means that this Tesco project is the topic of your question as well.
As far as your direct grammatical question, Therefore, sth could have been done merely says the action became possible. It is, however, a very awkward construction if the action was undertaken. It's so much easier to say, Therefore, sth was done that the awkward phrasing implies that it was never actually carried out.
In this particular case, the actions were undertaken and should simply be stated instead of avoided.
Once the project's objectives were established, planning could begin for its execution. The first task was to organise the work in such a way that its monetary and time costs could be easily overseen...
