So, I've started serious work on making a new version of Void Born now that most of the core technic mods have updated and 6.1 Dev Build is starting to shape up.
So here is a sneak peak at the new spawn location, ignore the ground I'm just building every major location in a separate flat mode map and merging it into one map at the last moment.
Don't worry, excruciating version will still give you your classic 1 block spawning place and puzzle just to find out how to start.
On the topic of invisible blocks, sorry, I have no idea what causes this or how to fix it, your best bet is to go to the bug forums. This is generally true for other bugs too unless its very specifically related to this map you have a much better shot at getting it fixed in the right place instead of this thread.