Each of the Vanguard frames has a single advantage over the others, regardless of what you put in with the BUK/module. IIRC, the Warden has speed, the Hoplite has hull points, the Harbinger has an S3 turret and the Sentinel has stealth. Right now the Sentinel stats are fubar but one supposes this will be fixed.
In addition you will be able to swap the guts of each into each other, so you can add the Harby torp package to the Sentinel if you like, but you lose the EMP and you don't get the Harby S3 turret since that is part of the frame rather than the module.
I have not seen an official CIG update of what the electronic warefare package aboard the Sentinel is eventually supposed to do, and I suspect they will never make good on the promise that it will mimick other ship signatures, but rather just leave the EMP in place. Also we still haven't seen what CIG plans for spike missiles, and that appears may never happen. Surely if they intended to stay with the original vision of distortion damage spike missiles and torps, they could easily have been implemented and tested by now. So I am suspicious of what they intend in the future on the EM warefare front. Originally the Arrester III missiles were slated to do distortion damage (hence the name) and there were no S1 or S2 missiles that could do this. Such was the plan to make spiking unavailable to smaller fighers that had no S3 missile capability. I think though, they may have bagged all of that since there has been no word since the introduction of the Sentinel.
According to the information on the BUKs the frame is the same and the changes from one version to the next are included in the "Combination Kit" (Or is it pack, I forget). For the Sentinel, Warden and Harbinger (maybe the Hoplite) with the kits, one Vanguard equals all Vanguards.
So for example a Warden or a Sentinel that applies the parts from the Harbinger kit would get the additional armor of the Harbinger (Specified in the original BUK and around 3.6, when the rework was being talked about) which would imply the change to speed and agility.
The turrets are swappable and should be included in the Combination kit. The Harbinger turret is supposed to have Ordinance Hardpoints instead of gun hardpoints, so shouldn't be able to equip size 3 guns, but that is a current workaround.
Like the Hornet Ghost, one would expect the Combination kit would also include stealth armor for the Sentinel, and the Warden/Harbinger kits would include the panels to make them not stealth.
The parts are supposed to be mix and match, so if you wanted the AR Cockpit of the Sentinel, the Torpedo module from the Harbinger and the Warden turret, with the Warden armor (and speed), on a Vanguard, you could do that, or any other combination.
The Hoplite was implied to be capable of handling combination kits, but that has never been officially stated, as far as I recall.
A set of Battlefield Upgrade Kits are also available for those who would like to keep their older Vanguard Wardens. The upgrade kits function as in-universe part sets which convert the existing ships to the variant’s specifications. This allows you to swap between the abilities of the Warden, Sentinel or Harbinger at will! The upgrade kits exist in world similar to the interior Retaliator upgrade pods and do not change the styling of the individual ships, just the weapons and other upgrades installed.
From:
https://robertsspaceindustries.com/comm-link/transmission/14915-Vanguards-And-Then-There-Were-Three
Edited to add: One other point, at this point in time owning a BUK does you no good. My Sentinel BUK doesn't give me the guns, the components, and of course not the module nor does it give me a Sentinel as a loaner.