Odd to need a spacer on a road 11, usually need a spacer for anything else on a road 11 freehub.
I take it the cassette is actually snug on the freehub without the need of a spacer?
The freehub length of circa 36.5mm tallys for road 11, the 45mm you mention though would give a smaller distance to the freehub seat, not longer, so shimming the cassette end would push it further still to the DS.(about 2mm total). [which is to say the opposite of your solution of shimming the thru axle if I understand correctly]
The poor shifting should be addressable by re indexing your mech though? Or is this a concern with a 1mm variance in chain line?
Shimming the thru axle end will simply push your dropouts wide by 1mm, this will “fix” the chain line I guess.
What I wonder is why the heck did Elite do 45 mm spacing when the standard is 46 mm?
The same reason mavic always made their hubs longer, that dt and shimano don’t have identical sizing etc. The standard is a manufacturer’s standard not an iso spec.