I do not think your misunderstanding anything, just have a factory rifle and a long throat is not a rare problem. The reason factories do this is so that they cover their rears in all shooting conditions. A long throat will drop chamber pressure with factory loads so that in very hot conditions the load will still be very safe, in cold temps, rather anemic to be honest!!
If you as them about handloads, they will tell you you should never hand load ammo because its far to dangerous to get it right...............
It is not uncommon to have to seat the bullets so long to get close to the lands that the loaded ammo will not fit in the magazine box. THis can be corrected with your Rem 700 simply by having a qualifies smith install a replacement mag box to offer you more length.
First thing to do is seat the bullets even longer until you determine just how long your throat is, then get your over all length and then decide if even the extended mag boxes would work. Then take it to your smith and talk it over to correct the problem.
Or shoot it as a single shot......
If you can afford it, rebarrel the rifle with a match grade barrel with a correctly designed throat. I would also recommend accurizing the receiver and bedding the rifle. She WILL be a shooter then if all is done correctly.