So you play it with hull down modifiers for units that are out of line of sight? It's not clear from your post. I don't think the issue is whether cover modifiers are worked out per unit or not (they are) it's when a unit actually counts as qualifying for a cover modifier (which is different from being IN cover).
The other ambiguity then being the way the placement rule is written, i.e. you can read it that you can only place a template over units that are in line of fire.
From the FAQs in the tournament pack rulebook, there are no placement restrictions for the additional templates (the original one must be in LoF and range, of course). To me, that contradicts what the 'Extra Barrage Templates' explanation states: in that part, because there is no other mention of LoF or range restrictions, it seems that sentence must be talking about the most recently mentioned LoF and range rules (i.e. must place the first template with at least one unit in LoF and range, therefore additional templates would have followed the same rule).
My long-winded point before was that, conceptually, there are two different ideas at play—maximising the number of units hit conflicts a bit with resolving hits on the units actually under the templates (and was only put in there, apparently, to stop 'barrage snipers').
For cover, there's nothing there that says you need to do anything special for determining modifiers, so for direct barrages, cover is presumably worked out from LoF (which contradicts with being able to hit units you can't see... but the next best thing would be applying the cover modifier, I suppose). For indirect barrages, the FAQ says that any intervening cover is ignored (which I think is extending the sentence about LoF too far, but one could go either way).
I think the only real way to fix these problems is to remove the contradicting ideas driving the rules, which is why I would personally prefer that the templates are only used for determining number of units hit and not which units are hit. With that simple change, as far as I can see, all the other problems are solved without any contradictions (and for indirect barrages, simply let them continue to ignore intervening cover to represent the vertical aspect).
Anyways, they're just some thoughts on the matter. Maybe they can help others work out a satisfactory solution!
PS: I finally found the sentence that says you allocate hits from front to back (of those units under the template)! Not so relevant, but it was a small victory for me
PPS: I forgot one thing for my proposed rule: the silly situation where you could kill a very distant unit from a different formation from the first because how close units in that second formation are to the firer. To get rid of that kind of 'spooky action at a distance', you could just make the LoF for secondary formations under the barrage come from the primary target unit rather than the firer, for all shooting purposes.