My concept for the three races is that it's the player's 'choice' to go towards Quests that will result in the transformation, but there will always be an out before you take the final 'plunge' and become a Super Mutant/Ghoul/Synth.
Super Mutant, you might get a quest shortly after leaving the Vault on your pipboy to investigate some weird shouting just to the north of Sanctuary, go up and there's some Super Mutants being led by a Primus, digging in the ground. The Sole Survivor gets jumped by a Super Mutant with a board and wakes up in a cage with several other prisoners, one of whom warns the Sole Survivor that the Super Mutants intend to 'dip' them all and turn the prisoners into more Super Mutants.
There's an option to either try to save yourself, thereby damning the other Prisoners as you use them as distractions, or damn yourself, distracting the Super Mutants so they can escape ... or if you're a high enough level, fight and kill the Super Mutants while the other Prisoners escape. If you sacrifice the Prisoners, nothing is ever mentioned except for people weeping about kidnapped family members and your own guilt, if you manage to fight off the Super Mutants, you're hailed as a friggin' hero by random NPCs who may have been fellow Prisoners or family/friends of those Prisoners.
And if you fail to kill the Super Mutants and get dipped, and stagger into the nearest town looking for aid, before the locals can shoot, or if you manage to make it to Diamond City and the Diamond City Security gets out their guns, one of the Prisoners you sacrificed yourself for runs up, shouting they know who and what you are, and explain to the trigger-happy locals what you did for them.
So you're tentatively allowed into the cities, but can now prove you're still a human being on the inside, however green and ugly you are on the outside.
Again, a totally optional quest you don't need for anything other than curiosity or a desire to play as a man (or woman!) trapped in a nightmarish body with unnatural strength and next to no fine motor skills, if a certain scientist is to be understood.
For the Ghoul, there's a abandoned military vehicle just near Sanctuary with radioactive barrels nearby. An easy fix would be to have 'experimental Rad-X prototype' as a pickup there that offers slightly better rad-immunity, but comes with a big warning that the producer takes no responsibility for side-effects, and the truck was dumped there by the soldiers after they were told they had to shoot up with the stuff in the presence of the radioactive barrels to test the effects and they decided to go AWOL.
Everything seems fine ... until you go to sleep and wake up in a pool of blood and jelly-like flesh. Step out from the bedroom and hear the people around you cry out in horror at what you have become!
At least the Rads won't be a problem anymore ...
For the Synth, maybe your Pipboy picks up an 'odd radio signal' from one of the abandoned shacks in the region just south-south-west of Sanctuary, a garbled distress call, and being the hero/mercenary/scavver you are, you rush over to either save somebody or pick over the corpses. Upon finding the shack, you instead encounter a Courser in a fire-fight with three individuals, and upon noticing you, the Courser immediately opens fire.
If you kill the Courser, well and good and you find out the trio knows one of them is a Synth, but nobody knows who, and they've been together for years and are determined to remain together until the day they all die, tell you they're making a run for the Commonwealth border and wish you good luck, leaving you with a Courser to loot.
If you fail to kill the Courser, and he's/she's very high level, well armored and equipped with the best laser-weaponry the Institute can create so for a low-level character right outta the Vault, it's going to be challenging at best, you get gut-shot and fall to the ground, your vision fading to black as you see the Courser come stomping over, looking down at you and going "Oh ... This is Courser X-26. Requesting emergency contact with ..." and your vision finally fades away ...
No, it can't end like this ... Shaun .... Nate/Nora .....
Suddenly, you're awake, lying in a dirty bed with the 'Legendary' Doctor NPC leaning over you, telling you how lucky you are to be here. When you ask what happened, the Doctor hems and haws but finally says that somebody dropped you off on her doorstep, and that you should thank your lucky stars to still be alive.
A close call, it seems, and displays how deadly the Institute is ... until you enter the Institute, and have a meeting with a certain NPC who smiles at you sadly and explains why it is you never seem to get tired anymore, and what really happened that day ...