If it is dangerous to fire the new ammo in the 88 rifles, the Germans didn't know it since they issued them to reserve units along with the "S" size ammo.
Here is the real story. The Model 1888 had a .311"* BORE diameter, and a .318" groove diameter. That meant the grooves were only .0035" deep, and lands started eroding quickly with the powder of the time. So the decision was made, c. 1905, to change the groove depth and adopt a larger diameter bullet, called the "S" bullet, of .323" diameter. Model 1898 rifles were recalled and re-barrelled, but there were millions of the old Model 1888 rifles in the war reserve. What to do?
Well, what they didn't do was to re-rifle those barrels. They found the new ammo gave high pressure not because of the bigger bullet in the barrel, but because of the lack of room at the old chamber neck for expansion of the case neck. If the case neck didn't have room to expand and release the bullet, pressure went to the danger point.
So all they did was to run a new dimension reamer into the chamber to expand the chamber neck, and fire the new ammo. They altered many millions of those rifles to accept the new clips (chargers) used with the Model 1898, marked an "S" on the receiver ring, and issued them to reserve units. There was no ammo confusion. New ammo was in chargers, old ammo was in en-bloc clips. If the clip fit the gun, the ammo was OK.
Later, during and after WWI, many of those altered Model 1888 rifles were given or sold to the Turks, and some collectors believe the Turks made the alterations. They didn't - the Germans did.
*Dimensions in inches for convenience; the Germans used the metric equivalents.