If it runs better with a larger gap, leave them there. The ignition system [ leads, insulation ] etc is obviously in good condition because the bigger gap needs a higher arcing voltage to fire the gap. If the system was in poor condition, you would get misfires etc. Instead, you found the car ran better.
The only downside is that the gaps will need to be checked & reset more often. You don't want the gaps to erode too much, to the point you get misfires.
0.054" is not that large for a medium compression, normally aspirated engine. GM recommended 0.060" gaps for the HEI when it was introduced.
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