The Molecular Level quest both is and isn't a point of no return, fundamentally it requires you to make a choice - what you do need to consider is that speaking to a faction will provide you the infiltration quest for the Institute but also make the equivalent quest for the other factions unavailable. It is possible to reconnect with the factions you didn't choose after completing Institutionalized though.
The game is seemingly inconsistent in warning you when you're about to make permanent changes to your faction reputations. The actual point of no return varies by faction alignment.
In the case of the Institute quest line, speaking to Allie to start the Mass Fusion quest will pop up a nice warning stating you're about to become permanently hostile to the Brotherhood of Steel. There isn't a subsequent warning when you do the same to the Railroad, you'll just get lots of failed quest spam if you've got quests outstanding but in fairness, the mission is specifically to kill the Railroad so...
For the Railroad, I believe the switch occurs silently at the start of the quest Precipice of War. I definitely didn't receive a message and the conversation to start Precipice of War seemed to flow continually from the conversation that ended Operation Ticonderoga - the Brotherhood of Steel just stormed in and then I got lots of quest failure spam.
For the Brotherhood of Steel, the mission that makes you hostile with the Railroad is Tactical Thinking.
Yes, once you've finished the "story" you can continue playing, but there will be less faction missions available because of who you destroyed in order to finish the story.
In my instance I chose to build my Signal Interceptor with the Minutemen which had no impacts on faction reputation but I'm told that choosing either the Brotherhood of Steel or the Railroad will impact faction reputation... (when I chose the Railroad I'd already killed several Brotherhood of Steel members so missed the opportunity to check this for myself).
I was then pretty loyal to the Institute and they tasked me with sourcing parts for their new power source which involved attacking the Brotherhood of Steel. Once this new power source was online the directorate became quite hostile in their intentions and demanded that the other factions were wiped out (excluding the Minutemen).
At the start of the Mass Fusion mission I was clearly prompted that starting this mission would result in becoming enemies with the Brotherhood of Steel (since you both need the mission objective from this particular level). As either of these factions you'll become hostile to the Railroad during the associated mission to destroy them.
It is possible to back out of your commitment to a particular faction later by re-aligning with the Minutemen to complete their quest line.
To Summarize:
Institute
Railroad
Brotherhood
The choice made at this point in the game marks the start of a quest line with each faction.
If you complete the Signal Interceptor with the Railroad, the quest you get to perform in the Institute is called Underground Undercover, in which you make contact with a scientist inside the Institute and coordinate an uprising of synths. Desdemona will be in charge and Tinker Tom will operate it.
If you complete it with the Minutemen you get a quest called Inside Job, which leads to the destruction of the Institute. If you choose one of the other factions to build the Signal Interceptor but later get kicked out of the Institute you're able to speak to Preston and continue with the Minuteman quest line. Preston will be in charge for the Minutemen and it will be Sturges who deciphers the blueprints.
If you build the Signal Interceptor with the Brotherhood of Steel you get the quest From Within. This quest tasks you with attempting to recruit an Institute scientist. Elder Maxson is in charge and the scientist is Proctor Ingram.
This choice doesn't lock you into any of these factions, that happens later in the game and is dependant on choices unrelated to this quest.
Best Answer
I have limited experience since I'm only on my second playthrough however so far I have observed -
If you join the Minutemen you'll end up allied with the Railroad and will end up destroying the Brotherhood of Steel and the Institute.
If you join the Brotherhood of Steel, you'll declare war against the Institute and Railroad while being allied with the Minutemen.
If you join the Railroad you'll be allied with the Minutemen and destroy the Brotherhood of Steel and the Institute.
If you join the Institute you'll be allied with the Minutemen and destroy the Railroad and the Brotherhood of Steel.
Regardless of which choice you make,