Well Bahasa Indonesia is based on Malay, it is standardized, tweaked a little, and then used to unite a nation consists of users of hundreds thriving ethnic languages to act as a uniting national language. There will be different vocabulary usages here and there, diction and accent are different, structures a bit off but yeah Indonesian most of the time will understand Malay. Especially when it is formal written Malay. For conversation, slow one may be ok, but fast Malay conversation will sometime confuse Indonesian. My own personal experience, when in Malaysia I just speak English because I worry about saying the wrong things, like Malay word for "Children" is "Budak" when in Indonesian "Budak" is "Slave"

I did a few courses bahasa Indonesia and one of my fellow students was studying Indonesian because she was moving to Malaysia. For her it was hard to find a Malaysian teacher or course and easy to find Indonesian so she did that. When she moved to Malaysia she did feel like she had a good basic knowledge. When I traveled in Malaysia myself I mostly spoke English, but using some Indonesian words did help me out in several situation to clarify things... What is the reason you want to learn Indonesian and/or Malay? That will probably help you decide which one to choose.