Rega spindle too short

.010 - .020" oughta do it. If forgoing the felt reveals enough of the spindle to use a clamp, you'll want to use a spacer of about 1 1/4" in diameter that fits over the spindle and protrudes above the level of the platter another .010" or so, depending on the record and how much spindle is available. If you can manage it, you'll like the result.

I was wondering what would be the downfall of not having the recess, because I don't think that I will be puting the mat back on soon.

I believe that the idea behind acrylic platters is that the impedance of acrylic is very close to that of vinyl, and with the LP placed directly on the platter surface and clamped, results in an effective LP thickness equal to the LP plus the platter (ie ~ 1 inch). Lacking solid contact you're not receiving this benefit.

That's the theory (and it's better explained in various artical on the web). My own experience is that placing the LP directly on the acrylic sounded profoundly better than with a mat. It also sounded better than my other table that had an alloy platter with felt mat.

I added a Funk Achromat to my table (which already has a 1" think acrylic platter). The Achromat impedance is supposedly perfectly equal to vinyl. While the spindle is too short to use the clamp now, the LP lays so perfectly flat on the Achromat that I think the clamp is superfluous. The sound is even better than with the LP clamped directly onto the acrylic platter. Further, I don't have to hassle with the clamp.

As for having the relief machined, if it were me I'd be tempted to do it - the only reservation I would have is whether the machining is done such that the platter remains balanced. And, not knowing how the IA platter is constructed, whether the machining could affect the structural integrity. And finally, if you ever get to the point you want to sell off your platter for an upgrade, the machining may diminish the resale value.

that's my 2 cents . . .
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I also agree about diminishing the resale value of the platter. How thick is the Acromat, I know I could research it, but I don't see the harm in asking. Like I said the sound with album placed directly on the platter is at least 75% better. Without the mat and record I have exactly 3/8" sticking up, would that be enough for the acromat?

The benfeit of the recess is the same regardless of the platter material. Snug record/platter mating is a very basic no brainer. It is a major factor in just about every aspect of the sound. Consequently, IMHO, clamping is major. I was just at Musical Surroundings listening to the $100k Clearaudio Statement table that uses a ring clamp as well as a center clamp. Even with this MASSIVE assault and its center clamp, the difference was not subtle when the ring clamp was added. Even with the Rega and it's felt mat the improvement was noticable when using the clamp from my Maplenoll as a record weight lending more transparancy, solidity and body.

the Achromat comes in 3mm and 5mm thickness. the 3mm mat setting on your IA platter may be the ticket. It provides the label relief w/o touching your platter. The 5mm may also work, but that would only leave 1/8" of spindle to center your LP.