Will the GM force the player to sit out because their character has an obligation? Will they force the table to decide between leaving one guy out or having everybody sit around and do nothing? If either of these is the case, they're being a bad GM. The alternative, though, turns the "flaw" into a piece of roleplay fluff at best. Inconvenient if you happen to get forced into your character's life, but meaningless at the table. (One could argue that having an income that's not reliant on being shot at is a good thing if you get lifeswapped, but that's neither here nor there.)
But there are plenty of alternatives that lie between the extremes of 'you can't take part in the session' and 'it doesn't affect you at all'.
For example you been at work all day and Shadowrunning all night. By the third day start applying some dice pool penalaties or rolls to see if he falls asleep during the boring stake-out as the Runner suffers from lack of sleep.
All Comicshorse's posts come with the advisor : This is just my opinion any difficulties arising from implementing my ideas are your own problem