I'm not quite sure I understand your question. If you have a scandoubler, there's no need to force the system to use "native" 31KHz modes. The purpose of DblNTSC is to get NTSC resolutions on non-NTSC monitors (i.e., 31KHz VGA monitors), but it's much more strenuous on the chipset and therefore considerably slower.
The scandoubler offloads all that work for you. With a scandoubler, NTSC HiRes Laced will give you the exact same resolution/functionality as DblNTSC HiRes NoFlicker but it will be much faster.
Other notes:
By "boot screen" I guess you mean the Early Startup Control menu (from holding both mouse buttons at boot)? That will always be plain NTSC (or PAL) until forced into another mode with a keyboard override. I'm not certain of this, but there might be ROM modules that can change it without an override, but those will first need to be kicked in as part of the startup-sequence or added to a custom-burned ROM. But again, none of this should matter if you have a scandoubler.
Maybe you know this already, but to permanently set your Workbench screenmode, the appropriate Monitor file needs to be in SYS:Devs/Monitors, which will enable it during bootup. To then switch to one of those modes, use SYS:Prefs/Screenmode. Select a mode and hit Save. It's a good idea to test the mode first to ensure the display can handle it.