Thank you for the DMG quote - I had to go SRD at work... finding stuff in there is always hard for me.
You're welcome to feel however you like, but this is in the Rules Forum, so it's about how the rules work as written. Personally, I agree with you - it does seem to penalize monster characters perhaps a little too harshly, but how we'd LIKE it done should go in House Rules. And actually, they ARE supposed to pay for their abilities both ways - LA as designed specifically slows down advancement of more powerful characters to keep them in line with their more 'normal' counterparts. Overall, I think the RAW are fair, though; many monsters (at least those people are generally interested in playing) have powerful supernatural, spell-like, and extraordinary abilities, as well as usually possessing powerful initial stat adjustments; from a balance standpoint, the rules keep more 'mundane' characters in line with monster PCs. Oddity races, like kobolds and goblins, are LA/HD +0, so they're just like mundane characters anyway.
And your example is not silly - NPC eladrin will last only a few encounters at most, if he even becomes involved in a combat at all. Your PC eladrin's abliities will effect the outcome of every encounter his party is invovled in - they're worth more than the NPC eladrin's abilities. If you're concerned about this discrepancy, there's an easy fix for it - make all your monsters with class levels like they were PCs. Both ways are legit by the RAW, it becomes just matter of taste.