They will if someone found the box is nearly in, they then (wrongly) use the bolts to pull the gearbox home, the alignment issue is normally the clutch friction plate and spigot bearing, using the bolts tends to force the friction plate to shift into the correct position as does rocking the gearbox from side to side/up and down, think about the amount of leverage and weight you have at your disposal.
A conservative guess I would say I have fitted over a thousand clutches over 50 years? And yes I did in the early learning days fit not one but two clutch plates in back to front, and of course used bolts to pull the gearbox home but, they were Ford Anglia's and Cortina's but never done any damage because the clutch plate would easily move into correct alignment with a bit of jiggling, but with heavy vehicles such as trucks and 4x4's the clutch pressure plate applies much more force, so damage can occur if alignment is not right, as an aside with newer vehicles now fitted with 'for life' clutches they rarely fail, but the damned dual mass flywheels do!!
regards
Dave