Currently it's hard-coded to a 500×200 default size, and if resized the new size doesn't survives a Geany restart. There's 3 things I could do:

  1. adapt that default size to the display scale (which is not the DPI)
  2. adapt to the height of a line, but that's tricky to compute
  3. allow configuration (or at least, restoring) default size

First option seems easy enough, and see below for a test patch.
Option 2 is probably best, but is clearly the most complicated of all.
Option 3 would be fairly easy, but I'm not sure if it's really practical.

Here's the patch for solution 1 (untested, as I don't have a HiDPI monitor at hand). Note that this requires a Geany GTK3 build with GTK >= 3.10 (fairly old by now) and you having set the scaling factor rather than just raised the DPI through the roof.

diff --git a/commander/src/commander-plugin.c b/commander/src/commander-plugin.c
index 9f8d0718..a138ec41 100644
--- a/commander/src/commander-plugin.c
+++ b/commander/src/commander-plugin.c
@@ -654,11 +654,16 @@ create_panel (void)
   GtkWidget          *scroll;
   GtkTreeViewColumn  *col;
   GtkCellRenderer    *cell;
+  gint                scale = 1;
+  
+#if GTK_CHECK_VERSION (3, 10)
+  scale = gtk_widget_get_scale_factor (geany_data->main_widgets->window);
+#endif
   
   plugin_data.panel = g_object_new (GTK_TYPE_WINDOW,
                                     "decorated", FALSE,
-                                    "default-width", 500,
-                                    "default-height", 200,
+                                    "default-width", 500 * scale,
+                                    "default-height", 200 * scale,
                                     "transient-for", geany_data->main_widgets->window,
                                     "window-position", GTK_WIN_POS_CENTER_ON_PARENT,
                                     "type-hint", GDK_WINDOW_TYPE_HINT_DIALOG,

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