box: fix certain cfg options initialized twice on recovery

Certain dynamic configuration options are initialized right in box.cc,
because they are needed for recovery. All such options are supposed to
be present in dynamic_cfg_skip_at_load table so that load_cfg.lua won't
try to set them again upon recovery completion. However, not all of them
happen to be there - sometime we simply forgot to patch this table after
introduction of a new configuration option. This patch adds all the
missing ones except checkpoint_count - there's no point to initialize
checkpoint_count in box.cc so it removes it from box.cc instead.