Yes, just use the upload via "Upload Using Programmer" in the file menu. (Wasn't that hard to find was it...)
But on most Arduino's like the Uno the bootloader isn't that big. I at least never managed to make Uno code that's to big for the Uno and I made some complex systems with it... But I must say, I don't know the Trinket. 2,7k for the bootloader seems to be idiotic large.