mc12345678:
Good, that's the developer mindset to consider the effects of the change desired. The goal would be yes, present the desired information to support those that don't allow javascript and how it would look if it was supported. As of I think ZC 1.5.4 maybe 1.5.3, the attributes.php file included an html tag to encompass the entirety of the attribute option being displayed. This allows javascript to "takeover" that option name which allows the attribute to be displayed as desired.
Now as to the latest question, first one back... is this product truly available without selecting either of the two checkboxes? If it is not possible for the product to "exist" without selecting a checkbox, then a checkbox is not likely the correct method of making a selection. Further, could the product ever exist if two or all checkboxes are marked? Again, if the answer to that is a no, then checkboxes are likely also not the type of selection to offer.
My recommendation in those two cases would be to use a radio button option. Further, based on the information presented in the image of two options being provided with no default preselected would recommend adding a third option value that is marked as default and display only. Having this configuration would require the customer to actively make a selection to support giving notification to the customer when attempting to add the product to the cart that they... well, make a selection.
Whether that default selection be shown on screen or not is up to css control.
Now, to the topic of the OCD of display "style", what about what is presented is desired to be changed? If it is for the two (or more) options to be displayed more in a list than a horizontal grouping, that is controlled by css more than it is through the file referenced, but more information is needed to be able to advise. Some of that additional information may include the settings for dynamic dropdowns (admin->configuration->dynamic dropdowns) as those settings could have an effect that I am not expecting.
Thank you much for the reply!
Good questions!
The product in question is just a sample and I forgot to add the preselected option when I created the attributes. But the final products will have the "original painting" option as pre-selected as the first option (if available) or the limited edition prints pre-selected in those instances where the original painting is sold.
In short, yes the product, which will be offered as original painting (1 unit) and limited edition print (several units typical 25-50 or more), can be purchased together in one go, if the customer desires, the reason why I decided to go for checkboxes instead of radio buttons. If I choose dropdown menus or radio buttons, customers wanting to add both options to the cart, would need to add them as two separate items in the cart, which isn't that big of a deal, but I thought checkboxes might give some flexibility. Perhaps I'm seeing this with the wrong pair of glasses? I have the tendency to use tools differently than the way they were intended to be used.
What I'm trying to accomplish in this case of the checkboxes, assuming I picked the right option, is move the "red dot" which marks the piece as sold, to the end or the right side of the price, as shown in the picture below.

I was able to pinpoint the line of code that displays the "sold" message which is controlled by the define PWA_OUT_OF_STOCK located on includes/classes/observers/class.products_with_attributes_stock.php at around line 368
if (empty($products_options_DISPLAYONLY->fields['attributes_display_only'])) {
$products_options_fields['products_options_values_name'] = $products_options_fields['products_options_values_name'] . PWA_OUT_OF_STOCK;
However I was unsuccessful at moving elements around to position the "sold" message, now displayed as a red dot, to the end. Again, I'm not good with php at all, I just play it by ear and through trial an error, tons of them. I'm only good at the design part and somehow manage for the most part to make things work the way I want them to.
These are the setting for the dynamic dropdowns as requested:

Thanks again for taking the time =)