Ok, I'll bite - lets assume you went with Protectorate/Aegis, do not have lockpick/hacking/pickpocket/stealth and do not wish to turn any neutral/friendly factions hostile. Lets even go for the worst case scenario and assume the pirates remained neutral after negotiations and you do not wish to turn them hostile either. You also maintained perfect relationship with faceless and thus not killed a single one. In other words I'm making all the assumptions necessary to come up with the highest XP deficit possible in this scenario.
Foul Mouth Wash - fair enough, you're not getting it, 2 XP lost.
Aegis Badge - fair enough, 4 XP lost.
Anarchist Symbol - you will get at least a dozen of these while doing the Protectorate questline.
Black Eel Insignia - 6 XP lost.
Pipe Junction - 9 XP lost.
Boats in Bottles - 14 XP lost.
Brzozplno Nebrechega Skontam - you will get this when gassing the drones, no skills required, no neutral/friendly factions turned hostile.
Dread Controller - 17 XP lost.
Infusion Tank - 20 XP lost.
Faceless Mask Fragment - 1 study from the corpse at the Beast's Lair, 25 XP lost.
JKK Pen - 28 XP lost.
Protectorate Insignia - you will get this at Hephaestus Research. As a Free Drone you can also get this without turning any neutral/friendly factions hostile since Protectorate is hostile by default at this point, so this doesn't belong on this list at all.
Praetorian Insignia - 31 XP lost.
Protectorate Dog Tags - you get those during the Renegades quest if you don't have persuasion. But fine, lets assume a peaceful approach - 34 XP lost.
Scrapper Insignia - looted from Elwood, it's a part of the scrappers questline, no one turns hostile. But fine, you intimidated him - 36 XP lost.
Sword Handle - technically obtainable with no skills by using sound distractions, but alright, let count this one as well - 39 XP lost.
Protectorare Can - you find one at Free Drones HQ when gassing them, so only 1 study missed - 41 XP lost.
Old Money - 43 XP lost.
You also miss the tri-monitor blueprint at JKK HQ - 46 XP lost.
You also don't get 2 medals and the Cutura from the Gray Army Base if you do it peacefully - 50 XP lost.
That's all I can think of off the top of my head.
In the end you lost a total of 50 XP right before taking the elevator to DC - which, assuming an otherwise thorough exploration, means you are at late lvl 28 at worst, early 29 at best. Not even a whole level behind the curve and going to hit 30 in the middle of DC at worst. I don't really see the supposed issue, especially considering just how many skill points you saved. Not a bad deal, honestly.