Early Commando Front Isolastic Questions

Vernier type will give tens of thousands of miles use if adjusted correctly. The softer rubbers are the best according to many owners. 

One big mistake many make that are not used to the verniers is fitting them the correct way around. On the front adjuster is on the right, rear is on the left, get it wrong and it's all tears as most notice when the rear wheel does not align with the rear loop.

Next is the adjustment, tighten until there is no gap, some read this to tighten until it can't be tightened any further then turn back a hole and half, which still leaves no gap.

With the vernier, to replace the rear involves some deep dismantling or 'hinging' the bike. Thankfully most bikes will need a deep overhaul by the time they need replacing so not really much of an issue. 

This job needs doing too often to want to faff around with shims — not so easy when the Isolastics are in place on a working bike. Also, you either need a stock of different sized shims, or face a wait while AN (or AN Other) supply the ones your measurements and calculations suggest are needed.

Note that the 0.010" clearance specified in the Workshop Manual can be treated as a maximum; subject to maintaining a minimum of 0.000", one can play around with the clearance to move around the rev range in which engine vibration is transmitted to the rest of the bike. This is cheaper and easier than experimenting with different compound rubbers.

On the question of your existing inner buffers, they should indeed incorporate free space BUT it should be between the buffers and the outer tube, not between the inner tube and the buffers. See the diagrams in AN's service notes available here: https://andover-norton.co.uk/en/techdb-category/8/frame-chassis.

I dare say the alternative arrangement might work OK, but since you have it apart you might as well ensure that it is as the designers intended. Given the front ones are as they are, what are the rear ones like?