I have an old spreadsheet that I was using for BOM computation (I've since discarded it in favor of a newer one for my own boards rather than Williams boards). When I look at that sheet I see a BOM of about $30 (does not include the ASIC nor the EPROM) for the Williams board. Some of the pricing I've used is old and may not take into account additional discounts from merchants for quantity purchases (i.e. it only computes the cost level of the actual number required).
Boards with more expensive BOMs are those that include transistors (TIP102 and TIP36C), high capacitance capacitors (e.g. 10,000uF@35V radial snap-in) and fuse cartridges. The System 11 CPU BOM I have in this sheet shows about $150 and the WPC-95 power driver BOM shows about $150 for everything. Each higher priced component increases the BOM fairly quickly.
If you calculate the bare board, BOM and labor altogether then Rottendog prices are actually reasonable. Some ICs on old boards are harder to find and if you buy an already manufactured board you don't have to deal with that (such as risk purchasing from eBay merchants). Rottendog also includes a warranty if something goes wrong. If you build your own ... you're on your own.
The reasons to build your own are those mentioned here. They are among others ability to select manufacturers of components , ability to socket all ICs and sense of accomplishment.