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This is my two issues with the crossword as well. Looking at the source material, I was expecting the relevant abbreviation to give rise to a thematic word or phrase within the grid, possibly before the next part of the instructions is applied. And I would have expected a definitive way to draw the second and third shapes.

There definitely appear to be two possible pathways for the two ovals. How do we know which is correct?

I have a full grid, the misprint messages and believe I have resolved the 2x2 blocks correctly – but the relevance of the "hideous truth" is still eluding me so far... can any kind soul who correctly interpreted this particular element offer a subtle nudge in the right direction?

At the point you're at, you will need google. To reveal the hideous truth, you have to choose the correct abbreviation. Try googling what each of them makes with the other 2x2 blocks. You'll definitely know when you've found it. I found googling the protagonists revealed by the misprints unhelpful.
I made many dreadful mistakes with arithmetic when decoding the 2x2 blocks, no reason why you would but worth checking again.
Alternatively, there will probably be a bit of the completed grid that is worrying you. Following the instruction related to the grid may suggest something there.

A real pleasure, this one. Beautifully detailed construction and presentation. Thank you, Shackleton.

I wasn't previously familiar with the subject, but the horrifying truth did rather leap out from the final larger squares. The nudge to which Jamesm artfully refers was nicely done. I agree that there seem to be two routes for the pair of shapes.

Still scratching for the definition (!) for 1d and parsing for 41a and 2 and 22d. Very happy to wait for nudges, though. Wouldn't want to spoil anyone's enjoyment of this.

Barnacle,
1d. is an historical word for a pirate (rover)
41a. 'save' means to reserve, or put aside. One letter is removed from the anagram fodder.
2d. is a compound anagram. An anagram of the answer + 'it' could form 'magic trick'
22d. (I + an abbreviation for 'say') goes inside 'lady'

Sorry, I gave the def. for 1a.
In 1d. a charger can be a large plate.

Thank you, Mattrom. Of course, of course, of course ... I did like 1a, too. Can't quite put my finger on why.

Interesting. My current assumption is that it’s the top left rather than bottom right. Definitely not sure though…

Once you've identified the work and calculated the correct large letters, it's clear which abbreviation to choose.