Can you control 2 mth starter sets independently (each with its own loop of track) on the same layout by using different starter set commander remotes?

My understanding is the DCS Commander Remote (that comes with the starter sets) will operate any DCS engine (that has the factory default settings.. i.e., that hasn't had its ID # changed via a "regular" DCS system).

And no, I don't think you can customize a DCS Commander Remote to work with a specific engine. 

Think of the DCS Commander Remote as basically a "conventional" transformer control that's wireless (& has a few more buttons that allow for access to PS2/3 features... but NOT including running multiple trains independently on the same electical block).

If you want to run two engines independently of each other, they'll need to be on separate electrical blocks, and the receiver for each block should be at different points of the layout (farther away from each other the better).  That way you can point the remote at the receiver for "loop A" and run that train, and point the remote at the receiver for "loop B" and run that train.   

No can do, I've tried it.

Yes, above idea is best bet.  The IR beam from the handheld-remote is fairly directional.  The receivers are omnidirectional (symmetrical red lens on top). If you operate from roughly the same position you can shield or mask the receiver lens to only "see" the line-of-sight IR beam coming from the remote rather than reflections off walls, ceiling, etc.

If you have two separate loops of tracks (forget about "blocks" or anything else), and you have each loop set up to be controlled separately by a DCS Remote Commander set (one handheld remote and one receiver for each loop), you will be able to use just one of the remote handhelds to control either or both of the loops.

HOWEVER, you will want to space the two receivers far enough apart, or "isolated" from each other in some way so when you do transmit a signal from the handheld remote to one loop's receiver it will not also be read simultaneously by the other loop's receiver.

The handheld remotes and receivers are the same in every starter set--they are not unique to any particular set in terms of the signal they send or any special coded identification in the engine.  For example, I use just one DCS Remote Commander set on my tinplate layout, and that one set (one receiver and one handheld) will operate any MTH starter set locomotive that has not been "altered" from the factory default setting.

Since the DCS remote Commander handled units use an infrared signal to "talk" to the receiver, and since that infrared beam is fairly close to being line-of-sight, you should not have a problem if the two receivers your are using are spaced far enough apart.  The truth be told, that line-of-sight thing is one of the things I don't particularly like about the DCS Remote Commander because I sometimes tend to forget that I must point the handheld at the receiver.  It takes some getting used to because if you point it in some other direction, the receiver won't respond (blinking light) and, as a result, the locomotive just goes on its merry way.

I tried that, but unless you had some really good spacing, the IR bounces off the walls (or something else) and controls the wrong train at times.

The solution to that, if it occurs, might be to construct a "shield" of some sort around the two receivers (both of which would still be placed as far apart as possible) so you really would have direct aim between the handheld and the respective receiver.

I don't have the space available on my layout for two separate loops, and would probably use the full DCS system on that layout if I did have the space, but I have found that the DCS Remote Commander, with the setup I currently have, is pretty darn directional.  On several occasions when I failed to aim the handheld remote almost directly at the receiver, the locomotive failed to respond.

I run my tinplate pike while sitting here at my home office desk since it is in the same room and just a couple of feet away from where I'm now sitting.  If I did have two independent loops, I would probably elevate the second loop and mount the second receiver at the opposite front end of the layout.

In any case, one handheld remote would control both loops.

If you're in one place, shielding them sounds like a plan.  I just was fooling around with them on two loops, so they were wide-open.  I actually always planned on getting the DCS system, but you've seen how well that is going in another thread!

Don't give up on that full DCS system, John!  Since I started using that system on my other layout some time ago, I haven't looked back.  However, I must admit that I'll be picking up the Lionel Legacy system this weekend and will also be installing it on that layout.  I want to be able to compare and contrast for myself the advantages and limitations of each system.

The "older" DCS system I have will be replaced with the updated version that is still in its box, and that older system will be installed on the tinplate pike to replace the DCS Remote Commander.

I haven't given up Allan, I've got too much bulldog blood.   It's on it's way to MTH, and I'm sure when the smoke settles I'll have a working DCS system.