Several approaches intended to run EMFTVM model to model transformations have appeared (see http://modeling-languages.com/executing-atl-transformations-java/).
However, all of these deal with EMFTVM transformations. I am in the case in which I have to run generated ATL transformations (with a HOT). Could I use a compiler from ATL to EMFTVM and use the Java code to run this resulting transformation afterwards?
Yes, check out http://git.eclipse.org/c/mmt/org.eclipse.atl.git/tree/tests/org.eclipse.m2m.atl.emftvm.tests/src/org/eclipse/m2m/atl/emftvm/tests/compiler/CompilerTest.java#n221 for inspiration (compiler output can be run without saving bytecode to disk). Based on this test code, you could build a standalone compiler.
The Eclipse-integrated compiler code can be found here: http://git.eclipse.org/c/mmt/org.eclipse.atl.git/tree/plugins/org.eclipse.m2m.atl.emftvm.compiler/src/org/eclipse/m2m/atl/emftvm/compiler/AtlToEmftvmCompiler.java
The Eclipse-integrated compiler requires you to save the bytecode in the Eclipse workspace.
Please note: the regular Q&A forum for ATL can be found at https://www.eclipse.org/forums/index.php/f/241/ You may get faster responses there.