I don't think you need to worry about that. If the bridge height and intonation was good before then just put the block between the body and trem block and recheck your intonation. That's all that matters. The bridge plate might not look level but all that matters is the vibrational transfer to the body through the trem block/wood block area.
Other option is to find a 3 inch or so bolt that will fit those threads. Thread the bolt into the insert and then take a hammer and tap the end of the bolt to push the insert further into the body. Then install your block.