There is no optimal solution to fix this that I've found, outside of removing all block checks for a bootstrap import, or including an entire Yacoin data directory, which is what I'm guessing Ron has done in yac048boot.zip? Either way removes the *mostly trustless nature of YAC. *Mostly, due to checkpoints still being a thing, but avoids someone having to download the entire block-chain from scratch so it's a trade-off.
That is what Ron has done. You should really check it out.
There is a legitimate point to be had in regards to how NFactor increases jeopardize the network--in addition to the bootstrap problem. The original idea behind the NFactor increases was to maintain asic-resistance and recruit more players and stakeholders as CPUs gain more and more of competitive advantage over GPUs.
The intent has not been served. It is time for YAC to consider a freeze at current NF or revert to NF16.