I've been comparing your system with the RAW system for the purposes of encounter design and noticed something along these lines. When it comes to large groups of same CR monsters, your system seems to underestimate the encounter challenge by one degree as compared to RAW.
For example, take a party of 4 characters of 8th level.
In your system, the PEL thresholds would be EASY (40%) = 12+ / MEDIUM (60%) = 19+ / HARD (80%) = 25+ / DEADLY (100%) = 32+
Whereas in the RAW system, the XP thresholds would be EASY =1,800+ / MEDIUM = 3,600+ / HARD = 5,600+ / DEADLY = 8,400+
First, they face a pack of 8 dire wolves. In your system this would be just an EASY encounter (PEL 16), whereas in the RAW system this would be a MEDIUM encounter (8 * 200 * 2.5 = 4,000 XP). Probably not a big deal, since the key difference between an EASY and MEDIUM encounter is the expenditure of healing resources.
Next, they face a pack of 14 dire wolves. In your system this would be a HARD encounter (PEL 28), whereas in the RAW system this would be a DEADLY encounter (14 * 200 * 3 = 8,400). And if it were 15 dire wolves it would clearly be a DEADLY encounter thanks to the monster multiplier. This is a more significant discrepancy because the difference between a HARD and a DEADLY encounter could be the difference between few / no PC deaths and multiple deaths / a TPK.
Which is the more accurate guideline? I don't know. I suspect for a well-equipped fully rested party of 4+ PCs with powerful area spells that your system is a bit more accurate. However, if the party is under-equipped, not fully rested, is of small size (thus with diminished force multiplier capacity), or lacks a caster with area spells, then I suspect the RAW system is a bit more accurate.
With the encounter difficulty changing in the new version of the Basic DMG, I am not sure the 40%, 60%, 80%, and 100% thresholds are still valid. There is also a differentiation between scaling the adjusted XP in both systems. So where you calculate the two systems matters, but you already pointed that out.
I use a spreadsheet, so I don't really care if the difficulty is calculated using PEL or RAW. The greatest strength of PEL in my opinion is that it provides a gradual, constant scaling of encounter difficulty with each new creature added. RAW has some nasty jumps in difficulty. Dire Wolves 3-6 add 400 XP each, but Dire Wolf 7 adds 1100 XP. A viable solution may be to introduce PEL's scaling into the normal XP budget system. But doing that on the fly would require a spreadsheet which is not something everyone is going to have when they are putting together an encounter. I have a feeling the PEL tables might still work, but they may need to be rebalanced.