List<Account> uniqueIdMatchAcc = new List<Account>();
if(allUniqueIDs.size()>0){
  uniqueIdMatchAcc = [Select id, unique__c From Account Where unique__c in :allUniqueIDs];
}
if(uniqueIdMatchAcc.size() > 0 ){ //if unique matches were found, feed Id's into registrationList created earlier
   for(Account uma : uniqueIdMatchAcc){
        for(registration crl : registrationList){
            if(uma.unique__c == crl.acc.unique__c){
                crl.acc.Id = uma.Id;
            }
        }
    }
}

Map<String,Account> uniqueIdMatchAccMap = new Map<String,Account>();
for(Account a: [Select unique__c From Account Where unique__c in :allUnique]){
    uniqueIdMatchAccMap.put(a.unique__c, a);
}
if(uniqueIdMatchAccMap.size() > 0 ){
  for(String unique : uniqueIdMatchAccMap.keySet()){
    for(registration rl : registrationList){
      if(unique == rl.acc.unique__c){
        rl.acc.Id = uniqueIdMatchAccMap.get(unique).Id;
      }
    }
  }
}