The sentence is very clear and not vague at all and besides Toriyama is a simple writer. Dragonball in general is a simple show. When something is stated it is what it is unless it is later implied it isn't or later changed/retconned either for plot purposes or for correcting a mistake or due to editorial influences or whatever. For example when someone is bluffing like e.g. Vegeta against Android 20 it was made clear it was a bluff later. Or when ideas/opinions are expressed through characters like Yamcha implying Kuririn is the strongest earthling it means that Kuririn IS the strongest earthling. You could argue “but yeah Yamcha was talking to Kuririn’s daughter and was lying” or “but yeah Yamcha didn't train for 7 years and he was not a reliable source” or “but yeah Yamcha didn't see Tenshinhan for a while to gauge his power” and other similar explanations but Toriyama in an interview clear cut stated Kuririn is the strongest which again proves that whenever in Dragonball something is stated even in a not 100% proven/certain way unless it is altered later on it actually is the in-universe reality. That applies to a number of other stated things like for instance Cell saying he was capable to destroy the solar system. Well he WAS…
Except that it isn't clear at all. You want it to be clear cut because it supports your theory, but the truth of the matter is that it can be taken in multiple ways. You yourself even gave a potential reason as to why he waited for three years before returning, as you commented about a rebuilt laboratory and power supply network. For all we know, Trunks didn't even bother to start charging the time machine again until after the lab and everything was already rebuilt/being rebuilt.
Your three year figure would be valid only if we knew for certain that he started charging the machine the moment that he got back from the past, but we don't know that. You can assume it all you want, but without a direct statement, it remains an inexact figure. However, Bulma's statement in the special chapter is an exact figure, because she is referring specifically to the amount of time it took to charge the time machine.
Well I know...it was because he had to wait 3 years for the time machine to get charged...
Again, the statement is vague and inexact.
No she also knew he would be at his house at any other later point.
And yet it was clear that she chose that spot for Trunks to meet Goku, and it was only upon Trunks stepping in to stop Freeza and Cold, thus revealing himself to the others, that he felt he had altered the past more than he wanted.
The events of the main timeline were not meant to alter completely prior to Trunks’ journey. It wouldn't make any sense as like in the main timeline the Z fighters could still sense Freeza’s approaching Ki and go there to confront him. Remember that the battle had to happen when Trunks appeared as Trunks said he was expecting Goku to be there to take on Freeza and King Cold. He didn't expect the battle to start 2 hours later (Trunks just calculated the 2 hours when was in the main timeline – possibly by tracking the spaceships or Goku's/Freeza's Ki) and it doesn’t make sense for Freeza to have had different plans in the original timeline from those expressed in the main one. Had in the original timeline Goku arrived using the spaceship instead of instant transmission, Freeza as planned would arrive to Earth 2 hours earlier and kill the population to demoralise Goku – something that we know for a fact that didn't happen in the original timeline. Therefore Goku did use IT to arrive on time and the most logical thing to say is that when the Z fighters arrived in the place, Goku was already there battling with Freeza – that is why Bulma was unaware of Goku’s ability to teleport.
Given that Trunks indicates his presence alone altered the timeline from what transpired in his, Cell's presence in the present timeline (having arrived a year prior to Trunks' first visit) could have caused an unseen deviation that made the Z Senshi go to investigate Freeza and Cold's arrival (or at the very least, make Bulma want to go see). Trunks' calculations on when and where Goku would arrive were based on when his ship arrived in the future, and if the events of Trunks' time played out the same way they did in the present, just with Goku arriving with Shunkan Idou to stop Freeza, then Bulma of Trunks' time should have known about Shunkan Idou if she were there to witness it all as she had in the present timeline.
After all, Vegeta and the others would have still inquired as to what happened on Namek and how he escaped, and more importantly it would have been asked how he managed to get to the battle in time without a ship, since it wouldn't have landed for another few hours. One can only logically assume that, for whatever reason, none of the Z Senshi (or Bulma, for that matter) went to investigate Freeza's arrival, as that's the only real way that Trunks being oblivious to Goku's ability to use Shunkan Idou would make sense.