If I'm not mistaken, I think writers have often had Lois fall in love with the persona of Clark that was viewed as the overall "real person" and not just the disguise. Hence why Lois was shown being in love with "Superman" back in the golden age since Superman was portrayed as the real person.
And I think the explanations with Lois crushing over the Superman persona during the period when Clark was portrayed as the real person was due to Lois viewing her crush over Superman as harmless since Superman was this larger than life character in her eyes that was seemingly unobtainable whereas Clark was literally right there and very real for her, thus being more cautious in order to avoid heading into a potential heartbreak.