-There is no real solution to serve in a true Torah following way under a secular army with total different priorities but just a stated promise to "accommodate" or make it work. There will always be two different priorities and who has the last word. The current army chaplains or rabbanut rabbis are nodding their heads on what the generals tell them are matters of pikuch nefesh etc. Genuine independent poskim will never just take their word for it of course and it will lead to all sorts of problems and frictions.
This.
The primary nafka minah is that the Charedi Rabbonim who send their constituents to serve - Mizrachim and similar - consider it important enough to compromise on this matter. Whereas, the Rabbonim that the Bnei Torah subscribe to (the ones that say "the biggest batlan shouldn't serve" for example) do not consider the matzav important enough to compromise on this.
Sigh... It would be absolutely lovely if there could be more tocho k'baro - more consistency in action - than there is. You can't say the army (the Chareid sections) is bad and then wander around Yafo because you are bored. But even when there isn't, it does not change the situation on the ground from the perspective of the gedolim.
As
@yfr bachur said, a completely separate army run by poskim of their ilk (without doing more than taking advice from the generals, deciding on their own re: kashrus, Shabbos and shmiras enayim) is the only way it could work.
Lastly, no one can claim that they would know how a Gadol would think about any matter without explicitly asking them. Quoting the previous gedolim (regardless of shita) and applying them to today's situation is irresponsible. Let the current Gedolim do that.