Yes, the laws don't care about who you bank with. If your "center of life" is in Germany, you are required to pay income taxes. Although "center of life" is not defined in detail in german tax law, there are a number of known indicators that are considered. For example, if you reside in Germany for 183 days per year or more, you are required to pay income tax on all of your income.
Having a personal account in a local bank may be a data point if you want to make a case about where you should be taxed but it won't automatically make you have permanent establishment or tax resident in Estonia
Yeah, highly recommend that. You can also contact Estonian folks who do understand the idea of running a co in Estonia and living elsewhere which isn't common in a country like Germany as local accountants there may be confused, there's a bunch of people on this list that have gone through at least some govt vetting https://e-resident.gov.ee/marketplace/service-providers/
I personally had a good working relationship with 1Office in particular and recommend them (wasn't a client but they were a partner when I worked for the e-Residency program and a buddy's GF works there who I trust and who does good work)