What many people forget is the fact, that the current time line is an altered time line and not the original one.
But what we know is, that Bacon changed something in the past, which cause a heavy alteration of the original time line. He also repeated certain events over and over again (time loops?) in which he included and trust MC more and more.
These two points that Cold Arctus wrote can be really central to understand , what it's going to happen in next update and from these two point i want to start to make some theories.
If the current time line is an altered one , all this time confusion could start from first day , because nobody can be sure from which point in the past happened something that messed up completely all thinks. But we can be pretty sure that the person that create this big caos in the time line should be Bacon. So not only the question must be what he really made Bacon , but when he made something to mess up thinks in a so big chaotic way.
My theory is that Bacon mess up completely think at first time travel he made and this provokes like a " Butterfly effect " in the other time lines and with next time jumps he has had the sole effect of making matters worse . He discovered that time travel can have some collateral health problem ( only after he understood that it's necessary to use some " protection " to be safe during a time jump) . For this reason he knows that his friend ( the protagonist ) have some health problems ( also the sexual attraction with girl can be explained like collateral effect ) .
My second hypothesis is that the last twist in the plot with the arrival of a second Bacon , is that this is not a Evil Bacon , but a Bacon from a different time line that he discovered before the right "medicine" to give to protagonist and save the correct going on of temporal lines . Like a Deus ex machina to unexpectedly resolve the plots and a apparently inexplicable situation.
I'm in the same opinion that Cold Arctus has , i don't think at all the Mc could be is own father or his own grandfather ; it would be not only a lazy explication and it could create a strange feeling for a player in future chapters of the game...
every explications must arrive from the first time jump for sure and this provoked some health issue . But now we come back to first question : what really made Bacon to mess up all thinks ? what could be the thing also small that he made to have a so big effect after in a so different time lines ? my hypothesis here is that in his first jump , for some reason Bacon met the other alternative Bacon , the same that it's arrived in last twist and one of the two version become completely crazy for this meeting. So for sure there is a good Bacon and a Evil one , but nobody knows who is really the bad one ....