I gather that you want to use the end mill because it has a flat bottom and the bore your machining does as well. What does the bottom of the hole look like after the indexable drill is finished? I use a normal 135 deg. drill for all my drilling and can quickly machine a flat bottom because of the point left by the drill bit. I think where your running into trouble is using "the largest size boring bar available". The bigger the bar the the less clearance you have for finishing that bottom. I've done what your talking about only because either I ran out of tool holders for the job and had a live vdi available, or tool to tool clearance problems didn't allow me to have something sticking out that far in z when it was out that far in X. Like a long boring bar in a tool block. I have never done it because it's faster or cheaper. That iscar end mill is what, $90 to $100? The insert is at most $13? The main spindle has 20hp and 150 lb/ft of tq and the live tool spindle is a paltry 7hp an 130 IN/LB. If you can get the job done faster and cheaper with the end mill than the boring bar, you know something I don't.
P.S., I gave up on iscars milling line. Too much money. $90 for a .5" finishred? They're cool, but not that cool. MSC's new ACCUPRO line is of the same quality at a fraction of the cost. I'm sure your Iscar rep will say different, mine did. You'll never get me away from their turning line though. I use their HELI-TURN WNMX insert for roughing and that is one mean insert. Same with their DO-GRIP, that thing is like a Swiss army knife.