Nah. Not really.
The 4th ed basic rule book (BRB) contains a lot of kool/useful/fun stuff that has been, perhaps for reasons of space and consiceness, left out of the 5th ed BRB.
So then, the idea that an army's codex 'trumps' the BRB is not too hard to cope with. ie a specific rule for a particular army stands even if it contradicts something in the BRB that everyone else has to abide by; for instance, Dark Eldar, living in the webway itself, are always the attacker in scenarios with attackers/defenders. No problemo.
And those things that are in the 4th ed BRB; combat patrols and Kill Team fights are still perfectly useable.
Indeed, I think, despite not actually playing much, that a games system that can handle Kill Team missions (you get one squad of expendable heros, I get a Bond Villan Lair) and Apocalypse scale games (>3000 points per side) without breaking is actually pretty good. I'm pleased that now I have game tables, scenery and armies, I can play immensely differring games with it all with the same rule set. Bonza.
One of the things that doesn't help is points. In Rogue Trader, there is a points list that gives the points cost for attributes, ailities and wargear. Nice.
Flicking through the newer codices, it is obvious that someone at GW noticed that certain combinations of things produced units that were either greater or lesser than these simple numerical points scores would suggest. And so the points scores that there now are, are so different that it's not easy to see where they come from. For instance, the Imperial Guardsman has dropped by two points in the 5th ed IG codex. This encourages the IG player to take more of them, simulating the type of army that the fluff suggests. Their stat line has not changed, the tweak to the points cost just made them cheaper.
So it's sort of hard to 'make stuff up' and give it an appropriate points cost. FW models always come with rules for their use somewhere, whether an Imperial Armour book, a pdf or in a soft back suppliment. There is always an aura of expense (in points cost) associated with these items when you look at the on line 40k community's comments on them. So that does not provide a good guide (although does provide a good 'upper' handrail).
Therefore the player is left with the 'counts as' option. Whatever it is that has been produced simply 'counts as' something from an existing army. Which is fine, but it does mean that whatever it has to 'count as' something from the codices that you actually possess/have access to. And if you wanted one of those you wouldn't have gone to the trouble of modelling something different in the first place - after all, the models are supposed to be WYSIWYG so you'd use a guardsman with a melta gun figure to represent a guardsman with a melta gun.
There are tweaks that one can reasonably extrapolate from a limited amount of source data to allow some creativity. As long it is the same mind/crerative genius using the same method for each of the new creations then the adjustments to each army should be comprable. It's a working practice and we're only playing beer and pizza games anyway. One might suppose that if a tournament organiser isn't going to allow (the already over priced) FW items, as they might not occur in the codex; they arn't going to allow home brew units either. Max Nix.