Channel 5 was indeed allocated to Worcester, but my recollection is that there was never actually a WTAG-TV construction permit issued, though the WSRS building on Asnebumskit was reportedly designed to handle a TV studio and transmitter.
There were a lot of different allocations proposals in the early years of TV that could have given Boston anywhere from two to six VHF channels. The politics were intense - the stations that got there first (WBZ and WNAC) didn't want more competition, political leaders in New Hampshire and central/western Massachusetts wanted their own stations instead of depending on Boston, and the FCC was still trying to figure out what the appropriate spacings should be between co- and adjacent-channel stations. (Oh - and by 1952 there were proposals to limit VHF use in the east to the big cities, with smaller markets in between being made all-UHF.)
So the allotment picture changed, over and over again, between 1947 and 1957, when the dial finally congealed into its permanent form. There were indeed some early proposals for Boston that included channels 9 and 13 (11 was then being used by WJAR). Once Providence's allocations were shifted from 11/13 to 10/12, that pretty much froze out any chance of using 11 or 13 in Boston, though there were attempts as late as the early 1960s to move channel 9 from Manchester to the Merrimack Valley.
In the end, Boston was slightly shortchanged; similarly-sized big cities tended to end up with five Vs (Chicago, Philadelphia/Wilmington) instead of the four that Boston got. But the flip side is that Boston was much more tightly spaced to other cities that became TV markets in their own rights: had the FCC, for instance, decided to make Rhode Island a UHF market, then at least one more V channel (13, probably) could have been added to Boston. (10 and 12 might then have been used to make Connecticut all-V, and Portland would probably have ended up with 12 instead of 13.)