but did what alt were betties and Ki-49s regularly flying at?
In respect of the raids on Darwin and northern Australia, the altitude was often above 25k and without putting a table together on it to know for sure, regularly 28k or greater. I included the link to that book as a lot of it is readable on Google books and it has just that type of information in quantity. It makes fascinating reading well beyond just the subject of raid alts. The raids over Darwin in 43 were generally high.
Burma was another theatre with different metrics. A lot of the raids there were in support of ground troops for instance. Low level attacks on forward airfields were a priority too. Raids on Rangoon by the Allies were mainly made at night. Japanese raids on Indian cities like Calcutta weren't forced to come in at great height. The defence was mainly Hurricanes and Mohawks and a couple of Republic Lancers thrown in for the high altitude work. The first Spitfire victory in the theatre was on the 8th November 1943 when a Ki46 was shot down at 25,000 feet over Chittagong.
Just getting right off subject, the Mohawks in this campaign apparently proved to be first rate front line fighters against the Ki43s. A number of pilots even claiming superior turn-fighting ability after engagements. There's mentions of this in Christopher Shore's "Air War for Burma", the third volume of the "Bloody Shambles" set.
While I'm at it, the Boomerang mention also raises interest. The CA12/13 Models were rushed to the front without a turbocharger as it was difficult and time consuming to integrate it during the emergency. The CA14 was the supercharged variant and it was never put into serial production. Delay killed it. The engines for it were supposed to come directly from the US, were ordered and just never arrived. An attempt to put the available locally produced R-2800 into that small airframe caused a number of problems including undercarriage failure. The CA14 was finally given an engine/turbo combo that gave it performance roughly equal of the Spit 5 - but 6 months too late.
By the time a solution was worked out in about July 1943 Spitfires were already blooded in action at the front. Crates of P40Es and Ns were piling up on the wharves just requiring assembly. CAC therefore abandoned the CA14 and worked on 2 new projects the CA15 "Kangaroo" and the not dissimilar CA17. You'd recognise the latter by it's more common handle - "P51 Mustang".