Unfortunately, LR doesn't provide plugins (including scripts) the ability to initiate merges.
If this is a task that will be repeated many times, the best you could do is use Autohotkey on Windows or a similar keystroke-stuffing program on Mac to semi-automate the steps, but that will be very fragile. Otherwise, consider the use of a scriptable program like Photoshop.
If this is a task that you'll just do once or a few times, here are some tips to accelerate the manual process. It could take you an hour or two to figure out how to apply the tips, so depending on how many photos you have, sometimes it's faster to just suck it up and do the job manually.
1. In each folder, stack the pairs of photos. You could select all the folders in the Folders panel and then use Autohotkey to stack each adjacent pair of photos displayed in Library Grid view.
2. Select all the folders in the Folders panel, then select all the displayed photos in Grid view, and do Photo > Stacking > Collapse All Stacks.
3. Select all the stacks and do Photo > Photo Merge > HDR. That will invoke HDR merge with the last used settings on each set of stacked photos, putting the result in the same folder. The progress will be displayed in a progress bar in the upper-left corner.
4. If you can put all the folders under the same parent folder, then it will be easy to select those folders in the foldes panel. Otherwise, if the folders have some distinguishing string in their names, e.g. "merge 1", "merge 2", etc. you can use the Filter Folders box at the top of the Folders panel to display just those folders (e.g. by filtering the folders for "merge").
Otherwise, rather than using a list of folders to start with, consider using a list of photo paths stored in a file. Then use a plugin such as Photo List Importer to select and filter just those photos in Grid View. Then use Autohotkey to stack them.
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