Thank you for the question! I agree that it is challenging to determine which is the best transcription of a shape in a spatial calculation.
First, you are right that the numeric indicator that is part of the square shape is not the same as numeric indicators for numbers; so it does not need to be aligned with them. Second, within a numeric passage, the shape indicator does not require a grade 1 symbol indicator, because numeric mode sets grade 1 mode.
I think the examples in the attached image (and repeated in the attached BRF) show viable options for transcribing this spatial calculation.
I cannot say anything about placement of the multiplication symbol, because that relies on what the print looks like and/or what the customer (e.g., a teacher) has requested. So, I have assumed that a) the print has the multiplication symbol to the left of the second multiplier and above the separation line.
As for alignment, no single cell of the square symbol needs to be aligned with any place value of the numbers, so I've simply started the shape in the first cell after the operation symbol and transcribed its components all unspaced.
Either individual numeric indicators or a numeric passage could be used for this calculation; it is up to you which works better within the larger transcription.
What do you think? Does this make sense, and will it work for you?