This answer has two parts. The first gives advice about a possible immediate action, while the second is a collection of things you might want to consider when talking to these companies. I mostly phrased those as questions you can try to answer for yourself.
My personal suggestion is to agree to the Skype call, but at the same time offer up that you planned to come to Germany a few weeks later anyway, and that you are happy to take a little detour to come and visit them to make the interview more personal. You can stress that you had already booked that trip, to make sure it doesn't sound needy.
Below is the reasoning behind my above conclusion. You can try to answer some of those questions for yourself for each of the companies. Who they are is essential to how they might react to such an offer.
To come up with a good approach, it's important to understand the situation as seen from from the company's side:
Why a phone/video interview?
To them, you are an applicant from another country. Inviting you to an interview costs them money for a flight, a hotel, and administrative time to schedule and book those together with you. There might also be a visa issue for you just to come to the interview (including invitation letters, possibly originals required at the German embassy in your country). That's a lot of hassle for one applicant, and they might have several.
It is therefore only reasonable for the company to ask for a phone/video interview first, to screen you before investing considerable more resources into you, just for a talk. After clearing that round, they will likely invite you for a face-to-face talk.
Why a face-to-face?
Of course you also need to take into account if those companies are willing to help with your work visa (if required, and depending on what kind of visa that would be), and if they offer a relocation package for your (and maybe your family). Those things are best talked about in person, but only after they have evaluated that you are a general fit.
What's your motivation for a face-to-face early in the process?
It might come across as that you are desperate to get to Germany and away from your current country, and could give the impression that you don't really care about the company as long as you get the chance to come to their country. You don't want to come across like that, even if it's true.
Who are those companies?
A young Berlin or Hamburg startup might probably go for that, and be happy to have you there without additional costs for them. A more conservative company, or a large corporation on the other hand will likely have a process to follow, and will not agree to that at all.
Of course you also need to take into account how quickly the companies want to fill those positions. Can they actually wait a few weeks just for you to come at your own, or were they maybe planning to invite you at their expense anyway a week after your Skype screen?
How to get there?
Are those all in the same city, or are you willing to alter your travel plans to go to different cities, just to get an interview there? Travel in Germany is easy and fast, but fast travel can be quite expensive. You can ask on travel.se in the germany tag if you need help with that. It's hard to say how a company reacts to your suggestion to alter your travel plans. If you for example planned to go to Cologne, a quick trip to Düsseldorf is just around the corner, but if you are going to Munich and tell them you can come to Berlin for the interview, it's not. That kind of distance is usually paid by the company for a domestic interviewee, and you suggesting to come might be seen as you asking them to pay for the trip.
As you can see, there are a lot of things worth thinking about, and it's hard to give a simple answer to this.