Excuse me, but have you even read the opening post?
No, this behaviour is intentional, because it's hard to calculate collisions between moving ship and players due to lag. So ships are ethereal while active. And no, all blocks are frozen when ship is on the move. You need to Disassemble it (I think it's K - click "Disassemble" or "\" key, but you can change actual keys in minecraft control options) to return the ship to the state of solid blocks. Once it's done, you can simply Mount your ship back (if you didn't alter its blocks) without Assembling it again. The ship will remember it's last assembly.
There was a mod that let you make actual 'subworlds' - independent groups of blocks that could move yet were solid and worked properly. But I think it's unavailable on the latest versions of Minecraft.
The subworlds your thinking of could it be Metaworlds? I think its updated for 1.7.2 and I believe, but may be wrong but I think it works for 1.7.10 as well.