People claim that you should not assign VLANs to SID0. However I have not found any examples of what can go wrong in the worst case.
It is clear that having a VLAN assigned to SID0 = CIST will make link changes concerning that VLAN have the entire spanning tree (all regions) recomputed. Having properly assigned the VLAN to an MSTI other than 0 would have limited the recomputation to the concerned region only.
This is the default working scenario in EOS and many customers run like this with no ill effects. Other than the issue you already noted and the fact that all the traffic will be on the common internal spanning tree path i see no functional problem. its merely a traffic planning issue. Functionally it would just be the same as RSTP.
Your traffic would also be on the single active forwarding path between any two Regions, which in the case of redundant links is determined by the currently prevailing settings relevant to SID0. So traffic planning again and scalability.
Most problems tend to stem from misconfiguration of vlan / sid on links and the fact that adding vlans to sids causes an interruption. A lot of people get around this by pre-conguring groups of vlans in advance that may be used in future. ( if that is your concern and reason for wanting to keep vlans in sid0 )
I find that generally you don't need more sids than the number of redundant paths so configuration needn't be complicated.