I have never heard of a UU against wiping one's baggage.
It isn't a question of being legal or not to wipe one's luggage. More a question of what you are allowed and not allowed to import. As everyone knows, or is supposed to know, if there is chalk marks on your luggage it is because the Custom believe something in the luggage should be checked. If spotted by a custom officer while removing the mark, even if it's in genuine innocence, you can be sure that it would be interpreted as an attempt of avoiding a control and a suspicious attitude. It would just reinforce their suspicion and interest in you, and it wouldn't put you in the best situation to keep what has attracted their attention at the scan.
The fact that there are custom officers in civil clothes profiling passengers is not a myth. I know it as a fact after discussing with officers from my kantor bea & cukai here in Manado. At each international flight arrival, they would have at least two officers mingling with passengers just to observe them. It is probably far easier for them here in Manado since we don't have much int'l flights landing at the same time in SamRat airport than it is for Soekarno hatta customs but still they must have quite a few staff just doing that.
I am fine with having my luggage marked, and I also understand that I am not allowed to enter the country with 10 bottles of spirit/wines and kilos of pork delicacies and cheese, which I have nevertheless always done for years. I just didn't try to hide it, didn't take the risk to arise more suspicion or to piss off anyone and trusted my ability to deal with them.
Dairies, pork and most food won't attract much interest and therefore it is very easy to persuade officers to let you keeping them in spite of the regulation. Alkohol is a bit more of a problem because any officers is aware of its high value in Indonesia and quite a few officers wouldn't mind drinking it if they don't think of reselling it.
Personally, over 20 years+ in Indonesia I had to fully open my luggage I think three times and I always kept everything which was in it, despite not being allowed to import most of what was inside. Once it took me probably over 30 minutes of gently haggling but the 2 others were smooth, just requiring a little discussion and a few please. Out of the three times, none required bribes despite probably being expected. Three times out of probably 100 or more international arrivals. It isn't much, especially considering that I can't remember 1 time when I wasn't way above what the regs permit to import.
My only failed "attempt" was an indirect one in fact. Two or three years ago my kids were coming back from France after a month vacation and I asked my mom to take 8 bottles of fine wine from my cellar to put them in my kids luggage. Knowing that I would be at reception of both the kids and the coppers I thought it wouldn't be a problem. I just didn't expect that, instead of spreading the bottles in the 4 coppers, my dear mom would put the 8 damn bottle altogether in the smaller copper my kids had.
What had to happen happened and my boy got flagged for his small copper. Bottles got removed by the custom officers and one of them escorted my boy to meet with me outside. I asked if I could talk to the boss in charge and the officer escorted us back inside to meet with him. The guy was nice, showed me the bottles they had seized and the regulation saying that 8 bottles of wine is a tad too much and that 1 liter of liquor per passenger ABOVE 18 y.o was the maximum allowed. I told him that I was fine with the seizure and that I totally understood the regulation. I also told him nicely that said regulation allows the owner of the seized goods to witness the destruction. The guy was smart and understood very quickly what I meant. I politely asked if I could get 4 of the bottles and confirm that unfortunately I won't have time to come to witness the destruction of the 4 others. We quickly agreed that 50% of the bottles given back to me was a fair deal for everyone. I had no time to waste to go to witness them destroying the bottles and the boss had very probably no intention to destroy them, but it is none of my business anyway. Also. even by loosing half of the bottles, the mathematics were still in my favor considering the price of alcool here. To me the important thing was that I could enjoy 4 bottles of wine I fully knew I was not supposed to have. And this is priceless.
I think that both immigration and custom officer (particularly the latter one) are generally nice folks, not so inclined in having rules and regulations followed to the letter as long as the "infraction" is innocuous/un-harmful, and finally rather easy to befriend with, having them being flexible and smooth with you. It has been my experience in 20+ years here and all over the archipelago. You have sometimes exceptions and can bump on an asshole like anywhere else in the world, but they are far from being a majority or even a strong minority.
At the end of the day, anyone can choose to do whatever they want with marks. In my personal case my luggage have been always pretty much covered with chalk. Recto, verso, side, it has often been as if the scan guys were trying to re-paint my red samsonite. Perhaps it's because each time a bunch of stuff triggered their interest at the scan, or perhaps it's simply because the material of the Samsonite made it difficult for the chalk to stick so the custom had to try to mark it all over? considering the amount of chalk, wiping it super clean wouldn't have been an easy and fast exercise anyway.