By any 'formal' problems...do you mean with Flag/Class?
The reason for using ISO rules, is that more often than not the boat being designed falls outside of "normal" rules for build/approvals. As a simple example, would you want to design your boat to the HSC rules and hence have the boat built to Class based upon these rules? Since a HSC boat must have a Flag and Class approval to obtain its permit to operate and insurance.
If your boat is a pleasure/luxury boat and does not require such 'formal' standards, then what do you do to show some measure of 'quality' or "compliance"?....the ISO have been developed purely for this, ie the smaller boat market and one off's, where such boats do not fall into very clear and obvious categories. These are now more formalised to prevent shoddy designs and workmanship becoming too prevalent, as they have been in the past...and now enforced by legislation
So, if your boat is just a pleasure-type boat, then so long as you are using ISO rules, to demonstrate compliance of some design "quality" for a client, then it should be acceptable.
However, it must always be remembered, rules, be they ISO, Class or otherwise, are just the MINIUMIM standards that must be complied with. They should never been seen as the be all and end all. Since many do not have the qualifications and/or experience to design from first principals, such rules are there as guidance, no more.