We've already discussed most of these, but I thought I'd clearly list all the options with examples for comparisons sake. I'll defer to those who have already commented on this thread to decide what is best since I don't do much C++ development myself.
1. target_dir/target_name/ClassName_jni.h
#include "base/base_jni_headers/ApkAssets_jni.h"
#include "chrome/android/features/autofill_assistant/jni_headers/AssistantOverlayModel_jni.h"
2. target_dir/Package Path/ClassName_jni.h
#include "base/org/chromium/base/ApkAssets_jni.h"
#include "chrome/android/features/autofill_assistant/org/chromium/chrome/browser/autofill_assistant/overlay/AssistantOverlayModel_jni.h"
3. Package Path/ClassName_jni.h
#include "org/chromium/base/ApkAssets_jni.h"
#include "org/chromium/chrome/browser/autofill_assistant/overlay/AssistantOverlayModel_jni.h"
A caveat of this option is that our code base will not be allowed to contain any duplicate java package/class name pairs for classes that use JNI (to avoid duplicate build outputs).
4. Java Source Path/ClassName_jni.h
#include "base/android/java/src/org/chromium/base/ApkAssets_jni.h"
#include "chrome/android/features/autofill_assistant/java/src/org/chromium/chrome/browser/autofill_assistant/overlay/AssistantOverlayModel_jni.h"
For most of these options, we'll probably have to tweak the DEPS include rules to allow all includes that match ".*_jni.h".