I believe the trick is to avoid having characters express an awareness of time unless you absolutely want to convey a large progression of time.
If the thief in the prison says something like: "I've been rotting here for months since you put me behind bars" then the player will be a bit confused about the time scale. It's better to just have the prisoner not mention or acknowledge time: "thanks to you I'm going to rot behind these bars".
If they player witnesses a progression of time in the world I believe they're going to naturally feel like they've missed out on events that may have happened (even if there aren't any in the game, they might feel like time was wasted). FF6 had the end of the world, the player wakes up as Celes and it feels like you've missed out because everyone is talking about how the world had ended. Imagine if you woke up as Locke or Sabin - characters who were busy during the aftermath - and how different that would feel for the player.
Half-Life 2 has a moment where the player is thrown a few days forward in time through a slow teleportation - this was a mechanic to speed up the story progression closer to its conclusion (story was famously for being heavily cut down), the player is told about this and I remember feeling like I had missed out on whatever else was going on in the world, the world moved forward without me.
If a building is under-construction for half the game and then it is complete by the second half, then have none of the NPCs acknowledge the time spent building it, just ignore the issue otherwise a player who gets there in an hour will have their sense of disbelief violated by defining strict time-line that they've been playing within (time is limited, it's probably best to not reveal that).
I would expect this writing and mechanics surrounding it naturally emerge through testing and seeing what feels right, but I can imagine some RPG Maker games out there having NPCs saying crap like "wow we just met yesterday!" despite the player resting in a tent over night about 20 times since meeting the NPC and talking to them this second time around.
Ultimately you're borrowing the player's time when they're in your game, so consider the player's personal internal clock (the one in their brain) as a hardware feature of your game and betray it in moments where you want the player to feel like they've been thrown forward in time (or backward, could confuse the player quite nicely by having NPCs grow younger and buildings disappear if that's what your story is about), otherwise pace your story as if it is a slave to it.
Games with internal clock functions are interesting because when the player walks away their actual real-time progresses, Animal Crossing makes use of this - however notice how Pokemon explicitly doesn't acknowledge the passage of real time despite having a real-time clock, Game Freak still want the player to feel like the game is on pause whilst they are away from playing it.
Popping out a baby is a hard definition of time (9 months) so I would handle that in a way the makes sure the game can take place anywhere within a 9 month period (that's a long time to play a game) - so I'd have the character already be rather pregnant or require an FF6 style move-forward-in-time to advance the pregnancy during the time that the player was "away" (coma, time travel, whatever). The same rule could probably be applied to building a house, make sure it's ambiguously near the end of construction early on so it's less jarring when it is complete, or do it when the player is "away".