UNDOCUMENTED MECHANICS
No — the target does not eat one full bolt before the rest fly outward. What the tables say is this:
The javelin thrust resolves first as physical weapon damage. At the same time 3 + (level ÷ 5) bolts spawn at the point of impact and fly outward.
Two columns decide the rest. These bolts have Activate = 3, meaning they are inert for their first 3 frames and cannot damage anything, and CollideKill = 1, meaning a bolt is destroyed by its first hit and never hits twice.
So a bolt only lands on the target if the target is still in its path after those 3 frames. That is exactly why Charged Strike is devastating against large monsters (bosses, super uniques) and unremarkable against small ones: a big collision box is still under the bolt when it arms; a small one is not.
For contrast, the Sorceress's Charged Bolt uses the same missile parameters but has no Activate at all — it can hit the moment it spawns.