I do not have a complete database of which yards did overhaul work on all the FLETCHERS during 1944-45. But I do have data from some from your list:
Overhauled at Bethlehem - SF yard:
DD-465 USS SAUFLEY, pictured October 44 with strake ... 31 August to 18 October 1944
DD-468 USS TAYLOR, pictured Jan 44, SF Bay area with strake ... 15 December 1943 to 26 January 1944
DD-471 USS BEALE, pictured at Hunters Point Jan 45 with strake ... 2 December 1944 to 18 January 1945
DD-478 USS STANLY, pictured with strake in SF Bay area Oct 44 ... 18 August to 12 October 1944
Others During 1944 and 1945 I know were overhauled at Bethlehem - SF yard (non-Bethlehem - SF built) before the Anti-Kamikaze mods:
DD-569 AULICK, doesn't appear to have gotten the strake ... 16 May to 19 June 1944
There likely were others including FULLAM and HUDSON that were overhauled at Bethlehem - SF that I have not yet cataloged.
DD-474 USS FULLAM, pictured in SF Bay area, Dec 44, with strake ... Don't know specific yard or dates yet
DD-475 USS HUDSON, pictured with strake in 1945, attached midships 20mm shields ... Don't know specific yard or dates yet
Anti-Kamikaze Mod units that Bethlehem - SF worked on:
DD-672 HEALY ... got strake ... 23 April to 10 June 1945
DD-528 MULLANY ... already had strake ... 30 May to 10 August 1945
DD-673 HICKOX ... got strake ... 8 July to 26 August 1945 (approx. departed yard about 3 September)
DD-674 HUNT ... got strake ... 8 July to 11 September 1945
Whether it was authorized or not, it doesn't seem to be a mod done by or required to be done at ALL yards to the class. Maybe it was a "tag" by Bethlehem - SF to "mark" the units of the class that THEY worked on.
All ships due for overhaul reported to Mare Island for removing ammo, etc. They were then assigned to a Navy Yard or a private yard depending on schedule and work required (normally decided well before they arrived in the area). Some private yards didn't have a drydock, so the ship may be assigned a period in a Navy or other drydock besides getting work done (sonar and/or dome replacement and general hull maintenance) at the assigned yard. Most (if not all) times the ship got her entire hull painted while in drydock. The bigger yards like Bethlehem had their own drydocks.
It is confusing, but Hunters Point ... first called Hunters Point Naval Dry Docks, then Hunters Point Navy Yard ... was renamed San Francisco Navy Shipyard at the end of the war. All ships were "SUPPOSE" to have post-mods photos taken. The private yards let the USN take the photos after they were done with the ship and an official USN inspection of the work was done (including a trial run). The ship would go to an USN Dock for provisioning the ship for return to service. The photographers could walk/drive down the row of docks to take the photos at the private yard or when the ship was at a USN dock. That is why these private yard overhauled ship photos have Hunters Point/SF or MINY labels on their photos. Unfortunately many ships didn't get photos taken during heavy volume periods or once the war ended. If someone didn't task the photographer with a task order, they did go out to take the photos.
As to the number of Overhauls in late 1944 into 1945, there are several factors in play here. "Normal" practice during the war was to "try" and have an overhaul about once a year "if possible". With the large number of FLETCHERS commissioned in 1943, there was a large number due for overhauls. Many of the earliest units also required major alterations to the latest configuration. Even though late 1944 through February 1945 was a heavy overhaul period ... the really heavy overhaul and REPAIR period was after the Kamikazes started doing their duty. Plus the fighting in and around the Philippines resulted in several FLETCHERS receiving mine damage. The yards in the San Francisco bay area were SO FULL of damaged ships of all varieties by June 1945, that repairs and overhauls for destroyers were assigned to places that until then had never worked on destroyers.