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The reason why people modded amps was because there wasn't that much available. You had Marshall, Fender and Mesa in the 80's. That's it. So people created their own sound. Nowadays, you have a whole industry based around amps that are modded Marshalls. In most cases, these built-from-the-ground-up-modded-Marshall-inspired amps sound BETTER than modded Marshalls.
With that in mind, not all mods are created equal. It all depends on what/how much you mod. Alot of mods are nothing more than 2 or 3 value changes and are easily reversed. Some guys take a metal-face Marshall and make it into a '68 or '67 by changing a couple values. That kind of stuff makes perfect sense to me. Old Marshalls had a good deal of inconsistencies between years. My '71 for example, is closer to a late 60's in values than what a '71 or '72 should be. So for me, all I'd have to do to turn my '71 into a '67 or '68 is change the filter caps. So would a 'best of breed' Super Lead really be considered modded? To a whacked out collector who looks for an unmolested all original Plexi? Yes! They'd want the filter caps (which need to be changed out every 10-15 years) to be original.
Everyone knows that early Marshalls were designed to be clean. Because Jim Marshall had no clue what he was doing and basically fucked up the design of the preamp, they distorted when you cranked them. However, when you have a 40 year old amp running at full-bore, you run the risk of blowing something up including your ears. So guys go on a quest to get the amp to sound cranked at non-cranked volumes. Some guys simply add a PPIMV so they don't go deaf. Other guys don't want to mod the amp and go the attenuator route. Both PPIMVs and attenuators have pluses and minuses.
But then there are folks that want a vintage amp to have the gain of a modern amp. Some people take a perfectly good 2203, punch holes in it for FX loops, add extra tubes blah blah blah. That makes no sense to me at all. The amp is no longer a Marshall. It's something else in a Marshall head shell. In most cases, it won't perform as well as a modern high gain amp and no longer have the vintage Marshall qualities. There are of course exceptions, but most of the heavily modded Marshalls I've played were a mess sound-wise. They had WAYYY too much uncontrollable gain. Squealed like stuck pigs. Didn't clean up at all.. etc... These were amps that were modded by FAMOUS dudes too.
So basically to sum up... Marshalls are old amps. They have a particular sound. If you don't like it, get something else. If it's too loud, and you feel like tinkering? There are ways to get it to sound good at low volumes. If you want a LITTLE extra gain, there are very easy ways to do that without ruining the amp. If you want extreme gain with a million voicing switches and line outs and fx loops, I would go with a modern amp. Why take an old amp that has it's own mojo and mess with it when there are so many options available?
That said, I prefer a stock Marshall + pedal. However, sometimes it's just not practical.
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It cant be modded cause somebodys bored... 
Best decision I every made. 